https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=HaendelNCBO Wiki - User contributions [en]2026-06-05T14:16:01ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=Clinical_and_Translational_Science_Ontology_Workshop&diff=11692Clinical and Translational Science Ontology Workshop2012-01-30T14:28:39Z<p>Haendel: </p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Clinical and Translational Science Ontology Tutorial and Workshop as part of its [http://www.bioontology.org/wiki/index.php/Meetings_and_Events series of training and dissemination events]. <br />
<br />
'''Venue:''' [http://hiltongardeninn.hilton.com/en/gi/hotels/index.jhtml;jsessionid=ALXZU454YC0FYCSGBJBNMQQ?ctyhocn=BWIAHGI Hilton Garden Inn Baltimore Airport]<br />
<br />
'''Date:''' <br />
<br />
:'''Tutorial: April 24, 2012''' <br />
:'''Workshop: April 25-26, 2012''' <br />
<br />
'''Organization:''' Barry Smith (NCBO / Buffalo), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)<br />
<br />
'''Registration:''' Please write to [mailto:phismith@buffalo.edu Barry Smith]<br />
<br />
The '''Tutorial''' will provide an introduction to ontology methods and technology for students and researchers. Topics highlighted in the tutorial will be of particular interest to individuals at institutions conducting clinical and translational research, including institutions which have or are interested in obtaining CTSA (Clinical and Translational Science Award) grants. <br />
<br />
The '''Workshop''' will provide an opportunity for those involved in ontology-related projects in the field of clinical and translational science to present on-going work and to review what has been achieved thus far. It will conclude with consideration of plans and strategies for enhanced coordination of ontology development initiatives in the field of clinical and translational science in the future.<br />
<br />
----<br />
<br />
=='''Tutorial: Tuesday, April 24, 10.30am-6pm'''==<br />
<br />
::::'''REGISTRATION FOR TUTORIAL IS NOW FULL -- PLACES STILL AVAILABLE FOR THE MAIN WORKSHOP (BELOW)'''<br />
<br />
For tutorial schedule and logistics information see [[Tutorial: Introduction to Biomedical Ontology for Clinical and Translational Research | here]]<br />
<br />
=='''Workshop Day 1: Wednesday, April 25, 9am-5pm (Draft Schedule)'''==<br />
<br />
:''Morning: The NCBO and Clinical and Translation Science Ontologies''<br />
<br />
::Mark Musen (Stanford / NCBO): Introduction and Welcome<br />
<br />
::Nigam Shah (Stanford / NCBO): [[Making Sense of Unstructured Data in Medicine using Ontologies]]: An Overview of NCBO Technology<br />
<br />
::::Changes in biomedical science, public policy, information technology, and electronic heath record (EHR) adoption have converged recently to enable a transformation in the delivery, efficiency, and effectiveness of health care. The true richness and complexity of health records lies within the clinical notes, which are free-text reports written by doctors and nurses in their daily practice. We have developed a scalable annotation and analysis workflow that uses public biomedical ontologies and is based on the term recognition tools developed by the National Center for Biomedical Ontology (NCBO). For further details see [[Making Sense of Unstructured Data in Medicine using Ontologies | here]]<br />
<br />
::Chris Chute (Mayo): Data Governance and Normalization within the Mayo Clinic Enterprise<br />
<br />
::::The principles and practice of data governance, as undertaken across the Mayo Clinic enterprise, will be reviewed and discussed, with particular emphasis on vocabulary harmonization and practice using NCBO tools for research. Extension to larger-scale consortia including the ONC HIT Standards Committee,SHARPn, ISO, and CIMI will be considered.<br />
<br />
::Shawn Murphy (Partners): Developing i2b2 Ontologies for the Long Haul<br />
<br />
::::In i2b2, we are developing methods and tools to help investigators answer research questions using secondary clinical data using a diversity of coded data from billing, decision support, laboratory, and electronic medical records, which can also be combined with data from clinical trials and high-throughput genomic instruments. Looking forward, the coding systems are potentially evolving and changing and yet data will need to be retained in their original coding systems to assure no loss in fidelity. Genomic data has similar challenges from the changing nomenclature and gene coordinates that may alter how similar genetic variants are named over time. We are pursuing a strategy with the National Center for Biomedical Ontology (NCBO) to allow a smooth adaption from one coding system to another so that queries remain valid despite these coding changes. New coding systems and mappings can be presented through NCBO web services, and these are transformed into hierarchies that reflect not only the sibling mappings but also the possibly broader and narrower meanings of the mapped terms.<br />
<br />
:''Afternoon: Major Ontology Initiatives relevant to Clinical and Translational Research''<br />
<br />
::Joseph M. Gunnels and Jihad S. Obeid (Medical University of South Carolina): An Ontology for Informed Consents and Other Research Permissions<br />
<br />
::::During the development of a comprehensive system for managing informed consents and permissions for research involving human participants, considerable effort is dedicated to laying down the foundation for a semantic web infrastructure and an underlying ontology to help standardize the development of electronic informed consents and the capture of underlying data. The objective is to allow future connections with other semantic web applications and pooling of data from multiple research projects.<br />
<br />
::Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): CTSA''Connect'': The VIVO and eagle-i Ontology Initiatives<br />
<br />
::::VIVO is a platform for managing researcher profiles at or across institutions in support of research expertise location. Eagle-i is a system that enables researchers to share and search for research resources. ShareCenter facilitates grass-roots sharing of information about expertise, activities, and organizational resources within the CTSAs and related organizations. All of these platforms enable publication of Linked Open Data. We describe the CTSAconnect project to harmonize and develop ontologies from these and other sources to support complex queries regarding expertise and activities of investigators, physicians, biomedical research resources, services, and clinical activities in the translational science domain.<br />
<br />
::Jessica Tenenbaum (Duke): Ontologies for Omic-Scale Datasets<br />
<br />
::::The use of "omic"-scale biomarkers to enable personalized medicine is becoming an increasingly important facet of translational biomedical research. Ontologies such as the Gene Ontology (GO) and the Ontology for Biomedical Investigations (OBI) can be used to facilitate data sharing, re-use, integration, and querying. This presentation will cover some of the more commonly used ontologies and how they may be applied to these ends.<br />
<br />
::Harold Lehmann (Baltimore): The Human Studies Database (HSDB) and the Ontology of Clinical Research (OCRe)<br />
<br />
::::Current efforts aimed at “tagging” research focus on study execution and results reporting. There is no existing ontology, however, for research methodology. Such an ontology would speed systematic reviews, aid in the assembly of research teams, and enable methodology-based decision support, among other use cases. The Ontology for Clinical Research is a national effort led by Ida Sim from UCSF currently validating its typology and implementing a number of OCRe-based tools. We will contrast this ontology with the Ontology for Biomedical Investigations and with the schemas of ClinicalTrials.gov and BRIDG.<br />
<br />
::Richard Scheuermann and Lindsay Cowell (Dallas): NLP-Based Mapping of Textbook Pathology to Ontology for General Medical Science (OGMS) <br />
<br />
::::Information about disease pathogenesis and disease course is available almost exclusively as free text and is therefore not easily accessible for query and analysis. We are addressing this problem by developing an ontology-driven NLP system for the mapping of basic pathology knowledge from free text to terms from OBO Foundry ontologies. In particular, we are using the Ontology of General Medical Science, with its tripartite structure of disease-disorder-disease_course, as the basic framework for the system. We will discuss preliminary results and describe planned use cases. <br />
<br />
----<br />
<br />
=='''Workshop Day 2: Thursday, April 26, 9am-4pm (Draft Schedule)'''==<br />
<br />
:'''9:00am EHR, Ontology and Interoperability'''<br />
<br />
::Rob Wynden (UCSF): The CTSA Health Ontology Mapper (HOM).<br />
<br />
::::The CTSA Health Ontology Mapper is an open source project to translate locally encoded patient encounter data, claims data and notes into standard biomedical terminologies by leveraging a real-time integration with the NCBO BioPortal REST services for access to biomedical ontologies and maps.<br />
<br />
::William Hogan (Arkansas): Referent Tracking and Demographic Data Ontology<br />
::::Numerous problems in the field of ontology are the consequence of (1) failure to pay attention to the instances about which we are collecting data, and (2) the lack of formal mechanisms to track instances and instance data, to relate instance data properly to representational units in ontologies, and to represent all these things unambiguously in the context of EHR data. This presentation will demonstrate Referent Tracking as a solution to these deficiencies with application to various particular use cases such as demographics data.<br />
<br />
:'''12:00pm Lunch'''<br />
<br />
:'''1:00pm Next Steps'''<br />
<br />
::How can we measure the value brought by ontology-based approaches? <br />
::How can we ensure high-quality and high-value approaches? <br />
::How can we promote a consistent approach across the CTSA consortium?<br />
<br />
----<br />
<br />
=='''Participants'''==<br />
<br />
Theodora Bakker (New York University Langone Medical Center)<br />
<br />
Olga Brazhnik (National Center for Advancing Translational Sciences, NIH)<br />
<br />
Mathias Brochhausen (Translational Research Institute, University of Arkansas for Medical Sciences)<br />
<br />
Chris Chute (Mayo / NCBO)<br />
<br />
Elaine Collier (National Center for Advancing Translational Sciences, NIH)<br />
<br />
Lindsay Cowell (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)<br />
<br />
Alexander Diehl (University at Buffalo)<br />
<br />
Michael Ferrante (University of Wisconsin Medical Foundation)<br />
<br />
Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)<br />
<br />
Solomon T. Garner, Jr. (Jackson State University / RCMI Translational Research Network Data Technology Coordinating Center)<br />
<br />
Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)<br />
<br />
Peter Good (National Human Genome Research Institute, NIH)<br />
<br />
Joseph M. Gunnels (Medical University of South Carolina)<br />
<br />
Melissa Haendel (Oregon Health & Science University)<br />
<br />
Karen Hanson (New York University Langone Medical Center)<br />
<br />
Daniel Harris (University of Kentucky Center for Clinical and Translational Science)<br />
<br />
Kathleen Hayden (University of Michigan Health System – Medical Center Information Technology)<br />
<br />
Darren Henderson (University of Kentucky Center for Clinical and Translational Science)<br />
<br />
William Hogan (Translational Research Institute, University of Arkansas for Medical Sciences)<br />
<br />
Pankaj Jaiswal (Oregon State University)<br />
<br />
Pathak Jyotishman (Mayo Clinic / NCBO)<br />
<br />
Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)<br />
<br />
Harold Lehmann (Johns Hopkins / Institute for Clinical and Translational Research<br />
<br />
Donald A. McClain (University of Utah Center for Clinical & Translational Science)<br />
<br />
Eric Meeks (University of California at San Francisco)<br />
<br />
Shawn Murphy (Partners Healthcare Research Computing / Harvard Medical School)<br />
<br />
Mark Musen (Stanford Center for Biomedical Informatics Research / NCBO)<br />
<br />
M. Theresa Perry (RCMI TRN Data and Technology Coordinating Center, Jacksonville State University)<br />
<br />
Taylor Pressler (The Ohio State University Center for Clinical and Translational Science)<br />
<br />
Mark Ressler (University at Buffalo)<br />
<br />
Michael Sayre (National Institute on Minority Health and Health Disparities, NIH)<br />
<br />
Richard Scheuermann (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)<br />
<br />
Amitava Shee (University of Michigan / Michigan Institute for Clinical & Health Research)<br />
<br />
Nigam Shah (Stanford Center for Biomedical Informatics Research / NCBO)<br />
<br />
Barry Smith (University at Buffalo / NCBO)<br />
<br />
Dagobert Soergel (University at Buffalo)<br />
<br />
Shumei S. Sun (Virginia Commonwealth University / CTSA Biomedical Informatics Core)<br />
<br />
Alisa Surkis (New York University School of Medicine)<br />
<br />
Umberto Tachinardi (University of Wisconsin Medical Foundation) <br />
<br />
Jessica Tenenbaum (Duke Translational Medicine Institute)<br />
<br />
David Towers (University of Wisconsin Medical Foundation)<br />
<br />
Patricia Whetzel (Stanford University / NCBO)<br />
<br />
Rob Wynden (University of California at San Francisco)</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Clinical_and_Translational_Science_Ontology_Workshop&diff=11587Clinical and Translational Science Ontology Workshop2012-01-05T21:00:12Z<p>Haendel: /* Participants */</p>
<hr />
<div>The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold a Clinical and Translational Science Ontology Tutorial and Workshop in its [http://www.bioontology.org/wiki/index.php/Meetings_and_Events series of training and dissemination events]. <br />
<br />
'''Venue:''' [http://hiltongardeninn.hilton.com/en/gi/hotels/index.jhtml;jsessionid=ALXZU454YC0FYCSGBJBNMQQ?ctyhocn=BWIAHGI Hilton Garden Inn Baltimore Airport]<br />
<br />
'''Date:''' <br />
<br />
:'''Tutorial: April 24, 2012''' <br />
:'''Workshop: April 25-26, 2012''' <br />
<br />
'''Organization:''' Barry Smith (NCBO), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)<br />
<br />
The '''Tutorial''' will provide a beginners' introduction to ontology methods and technology for students and researchers. Topics highlighted in the tutorial will be of particular interest to individuals at institutions conducting clinical and translational research, including institutions which have or are interested in obtaining CTSA (Clinical and Translational Science Award) grants. <br />
<br />
The '''Workshop''' will provide an opportunity for those involved in ontology-related projects in the field of clinical and translational science to present on-going work and to review what has been achieved thus far. It will conclude with consideration of plans and strategies for enhanced coordination of ontology development initiatives in the field of clinical and translational science in the future.<br />
<br />
----<br />
<br />
=='''Tutorial (Tuesday, April 24, 10.30am-6pm)'''==<br />
<br />
'''An Introduction to Biomedical Ontology for Clinical and Translational Research''' <br />
<br />
*Part I: Foundations of Biomedical Ontology<br />
<br />
*Part II: Ontology Technology: From the Semantic Web to the NCBO Bioportal<br />
<br />
See schedule [[Tutorial: Introduction to Biomedical Ontology for Clinical and Translational Research | here]]<br />
<br />
=='''Workshop Day 1: Wednesday, April 25, 9am-5pm (Draft Schedule)'''==<br />
<br />
:'''Major Ontology Initiatives relevant to Clinical and Translational Research'''<br />
<br />
::Chris Chute (Mayo): Data Governance and Normalization within the Mayo Clinic Enterprise<br />
<br />
::::The principles and practice of data governance, as undertaken across the Mayo Clinic enterprise, will be reviewed and discussed, with particular emphasis on vocabulary harmonization and practice using NCBO tools for research. Extension to larger-scale consortia including the ONC HIT Standards Committee,SHARPn, ISO, and CIMI will be considered.<br />
<br />
::Joseph M. Gunnels and Jihad S. Obeid (Medical University of South Carolina): An Ontology for Informed Consents and Other Research Permissions<br />
::::During the development of a comprehensive system for managing informed consents and permissions for research involving human participants, considerable effort is dedicated to laying down the foundation for a semantic web infrastructure and an underlying ontology to help standardize the development of electronic informed consents and the capture of underlying data. The objective is to allow future connections with other semantic web applications and pooling of data from multiple research projects.<br />
<br />
::Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): eagle-i and VIVO Ontology Initiatives<br />
<br />
::Jessica Tenenbaum (Duke): Ontologies for Omic-Scale Datasets<br />
<br />
::::The use of "omic"-scale biomarkers to enable personalized medicine is becoming an increasingly important facet of translational biomedical research. Ontologies such as the Gene Ontology (GO) and the Ontology for Biomedical Investigations (OBI) can be used to facilitate data sharing, re-use, integration, and querying. This presentation will cover some of the more commonly used ontologies and how they may be applied to these ends.<br />
<br />
::Harold Lehmann (Baltimore): The Human Studies Database (HSDB) and the Ontology of Clinical Research (OCRe)<br />
<br />
::William Hogan (Arkansas) and Werner Ceusters (Buffalo): Referent Tracking and Demographic Data Ontology<br />
<br />
::Shawn Murphy (Partners): i2b2-Specific Ontologies<br />
<br />
::Richard Scheuermann and Lindsay Cowell (Dallas): NLP-Based Mapping of Textbook Pathology to Ontology for General Medical Science (OGMS) <br />
<br />
::::Information about disease pathogenesis and disease course is available almost exclusively as free text and is therefore not easily accessible for query and analysis. We are addressing this problem by developing an ontology-driven NLP system for the mapping of basic pathology knowledge from free text to terms from OBO Foundry ontologies. In particular, we are using the Ontology of General Medical Science, with its tripartite structure of disease-disorder-disease_course, as the basic framework for the system. We will discuss preliminary results and describe planned use cases. <br />
<br />
::Nigam Shah (Stanford): [[Making Sense of Unstructured Data in Medicine using Ontologies]]: An Overview of NCBO Technology<br />
<br />
:::Changes in biomedical science, public policy, information technology, and electronic heath record (EHR) adoption have converged recently to enable a transformation in the delivery, efficiency, and effectiveness of health care. The true richness and complexity of health records lies within the clinical notes, which are free-text reports written by doctors and nurses in their daily practice. We have developed a scalable annotation and analysis workflow that uses public biomedical ontologies and is based on the term recognition tools developed by the National Center for Biomedical Ontology (NCBO). For further details see [[Making Sense of Unstructured Data in Medicine using Ontologies | here]]<br />
<br />
----<br />
<br />
=='''Workshop Day 2: Thursday, April 26, 9am-4pm (Draft Schedule)'''==<br />
<br />
:'''9:00am EHR, Ontology and Interoperability'''<br />
<br />
::Rob Wynden (UCSF): The CTSA Health Ontology Mapper (HOM).<br />
<br />
:::The CTSA Health Ontology Mapper is an open source project to translate locally encoded patient encounter data, claims data and notes into standard biomedical terminologies by leveraging a real-time integration with the NCBO BioPortal REST services for access to biomedical ontologies and maps.<br />
<br />
:'''12:00pm Lunch'''<br />
<br />
:'''1:00pm Next Steps'''<br />
<br />
::How can we measure the value brought by ontology-based approaches? <br />
::How can we ensure high-quality and high-value approaches? <br />
::How can we promote a consistent approach across the CTSA consortium?<br />
<br />
----<br />
<br />
=='''Participants'''==<br />
<br />
Participants will include:<br />
<br />
Mathias Brochhausen (Translational Research Institute, University of Arkansas for Medical Sciences)<br />
<br />
Alexander Diehl (University at Buffalo)<br />
<br />
Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)<br />
<br />
Joseph M. Gunnels (Medical University of South Carolina)<br />
<br />
Melissa Haendel (Oregon Health & Science University)<br />
<br />
William Hogan (Translational Research Institute, University of Arkansas for Medical Sciences)<br />
<br />
Harold Lehmann (Johns Hopkins / Institute for Clinical and Translational Research<br />
<br />
Shawn Murphy (Partners Healthcare Research Computing / Harvard Medical School)<br />
<br />
Mark Musen (Stanford Center for Biomedical Informatics Research / NCBO)<br />
<br />
Richard Scheuermann (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)<br />
<br />
Nigam Shah (Stanford Center for Biomedical Informatics Research / NCBO)<br />
<br />
Barry Smith (University at Buffalo / NCBO)<br />
<br />
Dagobert Soergel (University at Buffalo)<br />
<br />
Jessica Tenenbaum (Duke Translational Medicine Institute)<br />
<br />
Rob Wynden (University of California at San Francisco)</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=From_OBO_to_OWL_and_back&diff=11028From OBO to OWL and back2011-08-10T20:42:09Z<p>Haendel: /* Slides */</p>
<hr />
<div>This page is the location for downloads and instructions for the ICBO 2011 tutorial "From OBO to OWL and back again" to be held on July 27th.<br />
<br />
== Program ==<br />
<br />
The program, including suggestions for preparatory reading, can be found here:<br />
<br />
http://icbo.buffalo.edu/2011/TutorialF.pdf<br />
<br />
== Slides ==<br />
<br />
Slides from the whole ICBO anatomy workshop, including the obo to owl portion, are located here: <br />
[http://icbo.buffalo.edu/2011/slides/Anatomy%20Workshop/ anatomy workshop slides]<br />
<br />
[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.ppt draft slides ppt version] (may change slightly)<br />
<br />
[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.pdf draft slides PDF version] (may change slightly)<br />
<br />
== Test ontology ==<br />
<br />
[http://caro2.googlecode.com/svn/trunk/scratch/tutorial.obo tutorial.obo]<br />
<br />
Right click and choose 'save link as'<br />
<br />
== Software to install ==<br />
<br />
<br />
<br />
=== OBO-Edit 2.1 ===<br />
<br />
Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].<br />
<br />
Note - for (recent versions of?) Windows, the Java Virtual Machine is limited to 1G. If OBO-Edit fails to load in windows with the default memory settings, please re-install with memory set to 1024M.<br />
<br />
=== OBO to OWL conversion tool ===<br />
<br />
Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here:<br />
<br />
* http://code.google.com/p/owltools/downloads/list<br />
<br />
Installers are available for mac, windows and unix. After installation, you will have two applications:<br />
<br />
* The obo2owl converter<br />
* [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation The Obo Ontology Release Tool]<br />
<br />
=== Protege 4.1 ===<br />
<br />
Please install [http://protege.stanford.edu/download/protege/4.1/installanywhere/Web_Installers/ Protege 4.1 release candidate 5 (build 235)].<br />
<br />
This version of Protege should not need any configuring. <br />
<br />
Previous version required configuring to ensure labels (OBO names) are displayed in all components instead of IDs. Try loading an OBO file to test this (it should load straight in, even though the dialog box asks you to choose and OWL file). If you can only see IDs in <br />
the class hierarchy, then you should configure following the instructions here: <br />
<br />
http://code.google.com/p/caro2/wiki/Getting_started<br />
<br />
=== Optional ===<br />
<br />
Kent's test ontology from the anatomy workshop:<br />
[http://caro2.googlecode.com/svn/trunk/scratch/icbo-snomed-partonomy-test.owl icbo-snomed-partonomy-test.owl]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=8203Special:Badtitle/NS200:Revised 20082008-11-14T01:08:44Z<p>Haendel: polarity, angular placement, potency</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
<br />
Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.<br />
<br />
Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.<br />
<br />
Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).<br />
<br />
=== Functionality terms ===<br />
<br />
There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional <br />
is_a PATO:0001640 ! functional failure <br />
is_a PATO:0001642 ! partial functionality <br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001624 ! decreased functionality <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001511 ! non-functional <br />
<br />
<br />
The new hierarchy is:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional *** synonym related:impaired<br />
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality<br />
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure<br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001559 ! having extra function<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:<br />
<br />
is_a PATO:0001433 ! growth quality of occurrent<br />
is_a PATO:0002019 ! aplastic growth<br />
is_a PATO:0001490 ! heterochronic growth<br />
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.<br />
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.<br />
<br />
These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.<br />
<br />
=== Cellular Potency ===<br />
<br />
These terms were redefined to be more consistent with common usage and to make disjoint classes. <br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7845Special:Badtitle/NS200:Revised 20082008-10-09T23:00:32Z<p>Haendel: /* Functionality terms */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Functionality terms ===<br />
<br />
There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional <br />
is_a PATO:0001640 ! functional failure <br />
is_a PATO:0001642 ! partial functionality <br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001624 ! decreased functionality <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001511 ! non-functional <br />
<br />
<br />
The new hierarchy is:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional *** synonym related:impaired<br />
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality<br />
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure<br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001559 ! having extra function<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:<br />
<br />
is_a PATO:0001433 ! growth quality of occurrent<br />
is_a PATO:0002019 ! aplastic growth<br />
is_a PATO:0001490 ! heterochronic growth<br />
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.<br />
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.<br />
<br />
These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7844Special:Badtitle/NS200:Revised 20082008-10-09T22:59:07Z<p>Haendel: /* Functionality terms */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Functionality terms ===<br />
<br />
There were some redundant functionality terms as well as some that didn't quite adhere to the true path. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has added.<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional <br />
is_a PATO:0001640 ! functional failure <br />
is_a PATO:0001642 ! partial functionality <br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001624 ! decreased functionality <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001511 ! non-functional <br />
<br />
<br />
The new hierarchy is:<br />
<br />
is_a PATO:0001509 ! functionality <br />
is_a PATO:0001641 ! disfunctional *** synonym related:impaired<br />
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality<br />
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure<br />
is_a PATO:0001510 ! functional <br />
is_a PATO:0001625 ! increased functionality <br />
is_a PATO:0001559 ! having extra function<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:<br />
<br />
is_a PATO:0001433 ! growth quality of occurrent<br />
is_a PATO:0002019 ! aplastic growth<br />
is_a PATO:0001490 ! heterochronic growth<br />
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.<br />
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.<br />
<br />
These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7843Special:Badtitle/NS200:Revised 20082008-10-09T22:26:03Z<p>Haendel: </p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Functionality terms ===<br />
<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:<br />
<br />
is_a PATO:0001433 ! growth quality of occurrent<br />
is_a PATO:0002019 ! aplastic growth<br />
is_a PATO:0001490 ! heterochronic growth<br />
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.<br />
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.<br />
<br />
These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7829Special:Badtitle/NS200:Revised 20082008-10-08T20:46:03Z<p>Haendel: /* Plasty terms */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:<br />
<br />
is_a PATO:0001433 ! growth quality of occurrent<br />
is_a PATO:0002019 ! aplastic growth<br />
is_a PATO:0001490 ! heterochronic growth<br />
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.<br />
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.<br />
<br />
These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7828Special:Badtitle/NS200:Revised 20082008-10-08T20:30:00Z<p>Haendel: </p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7827Special:Badtitle/NS200:Revised 20082008-10-08T20:28:39Z<p>Haendel: </p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7826Special:Badtitle/NS200:Revised 20082008-10-08T20:27:29Z<p>Haendel: /* Color Improvements */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre><br />
<br />
=== Color Improvements ===<br />
<br />
'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7825Special:Badtitle/NS200:Revised 20082008-10-08T20:19:59Z<p>Haendel: </p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre><br />
<br />
=== Color Improvements ===</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7824Special:Badtitle/NS200:Revised 20082008-10-08T20:16:36Z<p>Haendel: /* Plasty terms */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7823Special:Badtitle/NS200:Revised 20082008-10-08T20:15:03Z<p>Haendel: /* Plasty terms */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:<br />
<br />
<br />
is_a PATO:0000141 ! structure<br />
is_a PATO:0000644 ! hyperplastic<br />
is_a PATO:0000640 ! dysplastic<br />
is_a PATO:0000942 ! underdeveloped<br />
is_a PATO:0000943 ! overdeveloped<br />
is_a PATO:0000645 ! hypoplastic <br />
is_a PATO:0001483 ! aplastic <br />
is_a PATO:0000117 ! size<br />
is_a PATO:0000586 ! increased size<br />
is_a PATO:0000584 ! hypertrophic<br />
is_a PATO:0000587 ! decreased size<br />
is_a PATO:0000585 ! hypotrophic<br />
--<br />
is_a PATO:0000070 ! presence<br />
is_a PATO:0000462 ! absent<br />
--<br />
is_a PATO:0001555 ! extra or missing physical and functional parts<br />
is_a PATO:0001557 ! lacking physical part<br />
<br />
<br />
In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7822Special:Badtitle/NS200:Revised 20082008-10-08T19:43:46Z<p>Haendel: /* Position / Placement */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement (synonym position)<br />
is_a PATO:0000132 ! spatial pattern (synonym pattern)<br />
<br />
Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.<br />
<br />
=== Plasty terms ===<br />
<br />
Melissa fixed these<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Revised_2008&diff=7821Special:Badtitle/NS200:Revised 20082008-10-08T19:08:44Z<p>Haendel: /* Position / Placement */</p>
<hr />
<div>* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]<br />
<br />
This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.<br />
<br />
== Friendlier Terminology ==<br />
<br />
current:<br />
<br />
is_a PATO:0001236 ! quality of occurrent *** <br />
is_a PATO:0001239 ! monadic quality of occurrent *** <br />
is_a PATO:0001240 ! relational quality of occurrent *** <br />
is_a PATO:0001241 ! quality of continuant *** <br />
is_a PATO:0001237 ! monadic quality of continuant *** <br />
is_a PATO:0001238 ! relational quality of continuant *** <br />
<br />
This terrified biologists and it was unneccessary to expose everyone to BFO terminology<br />
<br />
revised:<br />
<br />
is_a PATO:0001236 ! process quality *** <br />
is_a PATO:0001239 ! normal quality of a process *** <br />
is_a PATO:0001240 ! relational quality of a process *** <br />
is_a PATO:0001241 ! physical object quality *** <br />
is_a PATO:0001237 ! normal quality of a physical entity *** <br />
is_a PATO:0001238 ! relational quality of a physical entity *** <br />
<br />
The old terminology is supported as synonyms:<br />
<br />
is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]<br />
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]<br />
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]<br />
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]<br />
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]<br />
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]<br />
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]<br />
<br />
Definitions also improved (see file)<br />
<br />
<br />
<br />
== Ontology Content Changes ==<br />
<br />
Melissa and Chris made various merges, new terms and graph rearrangements<br />
<br />
=== Single is_a hierarchy ===<br />
<br />
Everything now has a single [[is_a]] parent<br />
<br />
=== Shape Hierarchy Improvements ===<br />
<br />
Current PATO has a flat list of shape terms, many of which have similarities in reality<br />
<br />
In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.<br />
<br />
A lot more work is probably needed here<br />
<br />
Sample of new hierarchy:<br />
<br />
is_a PATO:0002007 ! convex 3-D shape<br />
is_a PATO:0001357 ! pulvinate<br />
is_a PATO:0001865 ! spheroid<br />
is_a PATO:0000409 ! oblate<br />
is_a PATO:0001866 ! prolate<br />
is_a PATO:0001891 ! ovate<br />
is_a PATO:0001872 ! cuboid<br />
is_a PATO:0001873 ! cylindrical<br />
is_a PATO:0001874 ! discoid<br />
is_a PATO:0002008 ! concave 3-D shape<br />
is_a PATO:0000948 ! heart shaped<br />
is_a PATO:0001409 ! spindle-shaped<br />
is_a PATO:0001871 ! reniform<br />
is_a PATO:0001876 ! dumbbell-shaped<br />
is_a PATO:0001879 ! U-shaped<br />
is_a PATO:0001882 ! limaciform<br />
is_a PATO:0001883 ! clavate<br />
is_a PATO:0001890 ! tripartite<br />
is_a PATO:0001200 ! T-shaped<br />
is_a PATO:0001201 ! Y-shaped<br />
is_a PATO:0002009 ! branchiness<br />
is_a PATO:0000402 ! branched<br />
is_a PATO:0001784 ! bifurcated<br />
is_a PATO:0001967 ! actinodromous<br />
is_a PATO:0001968 ! parallelodromous<br />
is_a PATO:0001969 ! craspedodromous<br />
is_a PATO:0001970 ! brochidodromous<br />
is_a PATO:0001971 ! cladodromous<br />
is_a PATO:0001972 ! reticulodromous<br />
is_a PATO:0000414 ! unbranched<br />
<br />
previously many of these terms went directly under "shape"<br />
<br />
=== Position / Placement ===<br />
<br />
The old hierarchy was:<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000060 ! pattern<br />
is_a PATO:0000132 ! spatial pattern<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0001032 ! position<br />
<br />
<br />
In the new hierarchy, placement is a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).<br />
<br />
<br />
is_a PATO:0000051 ! morphology<br />
is_a PATO:0000140 ! placement<br />
is_a PATO:0000132 ! spatial pattern<br />
<br />
=== Plasty terms ===<br />
<br />
Melissa fixed these<br />
<br />
== Absent and friends ==<br />
<br />
See for summary of issues [[PATO:Absent]]<br />
<br />
Current PATO has this:<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0000068 ! qualitative<br />
is_a PATO:0000070 ! presence *** <br />
is_a PATO:0000462 ! absent *** <br />
is_a PATO:0000463 ! conspicuous<br />
is_a PATO:0000464 ! inconspicuous<br />
is_a PATO:0000467 ! present<br />
is_a PATO:0001241 ! quality of continuant<br />
is_a PATO:0001238 ! relational quality of continuant<br />
is_a PATO:0001555 ! extra or missing physical and functional parts *** <br />
is_a PATO:0001556 ! lacking function<br />
is_a PATO:0001557 ! lacking physical part<br />
is_a PATO:0001559 ! having extra function<br />
is_a PATO:0001560 ! having extra physical parts<br />
is_a PATO:0001568 ! having decreased function<br />
is_a PATO:0001569 ! having decreased physical parts<br />
is_a PATO:0001905 ! having physical part<br />
<br />
Issues:<br />
<br />
* no way of correlating 'absent' annotations with 'lacking physical part' annotations<br />
* confusing<br />
<br />
The revision attempts to fix this. <br />
<br />
The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)<br />
<br />
/ PATO:0000001 ! quality<br />
is_a PATO:0001241 ! physical object quality<br />
is_a PATO:0001238 ! relational quality of a physical entity c<br />
is_a PATO:0001555 ! has or lacks parts of type *** c <= n<br />
is_a PATO:0001905 ! has normal numbers of parts of type c = n<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n<br />
is_a PATO:0002000 ! lacks all parts of type c = 0<br />
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)<br />
is_a PATO:0002001 ! has fewer parts of type 0 < c < n<br />
is_a PATO:0002002 ! has extra parts of type c > n<br />
<br />
The same, with definitions:<br />
<br />
is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]<br />
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]<br />
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]<br />
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]<br />
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]<br />
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]<br />
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]<br />
<br />
Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:<br />
<br />
is_a PATO:0000070 ! presence or absence in organism *** <br />
is_a PATO:0000467 ! present in normal numbers in organism<br />
is_a PATO:0000470 ! present in greater numbers in organism<br />
is_a PATO:0001473 ! duplicated<br />
is_a PATO:0001996 ! absent from or present in fewer numbers in organism<br />
is_a PATO:0000462 ! absent from organism<br />
is_a PATO:0001997 ! present in fewer numbers in organism<br />
<br />
These are linked via the reciprocal_of relation. This is best seen in OE:<br />
<br />
[[Media:pato-absent.png]] (click for graph)<br />
<br />
Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.<br />
<br />
== New Relations ==<br />
<br />
=== Sub-qualities and has_part ===<br />
<br />
<pre><br />
[Typedef]<br />
id: has_part<br />
name: has_part<br />
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]<br />
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'<br />
created_by: cjm<br />
creation_date: 2008-08-12T03:01:56Z<br />
</pre><br />
<br />
=== Magnitudinal Relations ===<br />
<br />
We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.<br />
<br />
We do not use this function directly in PATO. However, the function is used to define two new relations:<br />
<br />
<pre><br />
[Typedef]<br />
id: increased_in_magnitude_relative_to<br />
name: increased_in_magnitude_relative_to<br />
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:14Z<br />
<br />
[Typedef]<br />
id: decreased_in_magnitude_relative_to<br />
name: decreased_in_magnitude_relative_to<br />
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]<br />
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'<br />
created_by: cjm<br />
creation_date: 2008-08-12T05:20:34Z<br />
</pre><br />
<br />
=== has_cross_section ===<br />
<br />
Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:<br />
<br />
<pre><br />
[Typedef]<br />
id: has_cross_section<br />
name: has_cross_section<br />
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]<br />
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round<br />
created_by: cjm<br />
creation_date: 2008-08-11T11:37:34Z<br />
</pre></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7101RO:Main Page2008-05-20T19:13:43Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is ''homologous_to'' continuant Y in taxon B when both are genealogically ''descended_from'' continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is ''homologous_to'' Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism <br />
<br />
- x1 is an anatomical structure <br />
<br />
- x1 part_of y1<br />
<br />
- y2 is an organism <br />
<br />
- x2 is an anatomical structure <br />
<br />
- x2 part_of y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D '''part_of''' some organism which is part of species R<br />
<br />
All instances of continuant E '''part_of''' some organism which is part of species S<br />
<br />
X is ''homologous_to'' Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z<br />
<br />
<br />
Note: The all/some looks wrong in the first 3 sentences of this definition Perhaps make third sentence '...MRCA all A and all B ? (comment added by David OS).<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7100RO:Main Page2008-05-20T19:12:16Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism <br />
<br />
- x1 is an anatomical structure <br />
<br />
- x1 part_of y1<br />
<br />
- y2 is an organism <br />
<br />
- x2 is an anatomical structure <br />
<br />
- x2 part_of y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D '''part_of''' some organism which is part of species R<br />
<br />
All instances of continuant E '''part_of''' some organism which is part of species S<br />
<br />
X is ''homologous_to'' Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z<br />
<br />
<br />
Note: The all/some looks wrong in the first 3 sentences of this definition Perhaps make third sentence '...MRCA all A and all B ? (comment added by David OS).<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7099RO:Main Page2008-05-20T19:08:49Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism <br />
<br />
- x1 is an anatomical structure <br />
<br />
- x1 part_of y1<br />
<br />
- y2 is an organism <br />
<br />
- x2 is an anatomical structure <br />
<br />
- x2 part_of y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D '''part_of''' some organism which is part of species R<br />
<br />
All instances of continuant E '''part_of''' some organism which is part of species S<br />
<br />
X is ''homologous_to'' Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z<br />
<br />
<br />
Note: The all/some looks wrong in the first 3 sentences of this definition Perhaps make third sentence '...MRCA all A and all B ? (comment added by David OS).<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7098RO:Main Page2008-05-20T19:04:56Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism <br />
<br />
- x1 is an anatomical structure <br />
<br />
- x1 part_of y1<br />
<br />
- y2 is an organism <br />
<br />
- x2 is an anatomical structure <br />
<br />
- x2 part_of y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X '''part_of''' some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y '''part_of''' some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z '''part_of''' some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D '''part_of''' some organism which is part of species R<br />
<br />
All instances of continuant E '''part_of''' some organism which is part of species S<br />
<br />
X is ''homologous_to'' Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X '''descended_from''' some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y '''descended_from''' some instance of Z<br />
<br />
<br />
Note: The all/some looks wrong in the first 3 sentences of this definition Perhaps make third sentence '...MRCA all A and all B ? (comment added by David OS).<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7096RO:Main Page2008-05-20T16:32:20Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
<br />
- y1 is an organism <br />
<br />
- x1 is an anatomical structure <br />
<br />
- x1 part_of y1<br />
<br />
- y2 is an organism <br />
<br />
- x2 is an anatomical structure <br />
<br />
- x2 part_of y2<br />
<br />
- y2 is a parent of y1<br />
<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7095RO:Main Page2008-05-20T16:31:08Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Type level relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
- y1 is an organism <br />
- x1 is an anatomical structure <br />
- x1 part_of y1<br />
- y2 is an organism <br />
- x2 is an anatomical structure <br />
- x2 part_of y2<br />
- y2 is a parent of y1<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7093RO:Main Page2008-05-20T06:35:27Z<p>Haendel: </p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if) <br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
x1 directly_descends_from x2 iff there are y1, y2 such that:<br />
- y1 is an organism <br />
- x1 is an anatomical structure <br />
- x1 part_of y1<br />
- y2 is an organism <br />
- x2 is an anatomical structure <br />
- x2 part_of y2<br />
- y2 is a parent of y1<br />
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2. <br />
<br />
<br />
that is part of organism y1 descends_from structure x2 that is part of <br />
<br />
<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7092RO:Main Page2008-05-20T05:32:40Z<p>Haendel: /* Since this definition includes 'descended_from', we've been discussing the following more extensive definition: */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7091RO:Main Page2008-05-20T05:14:40Z<p>Haendel: /* Since this definition includes 'descended_from', we've been discussing the following more extensive definition: */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
instance-level: a genealogical descends from a if a is a child+ of b<br />
class-level: Taxon A genealogical descends from Taxon B if for all a in A, a genealogical descends from some b in B.<br />
<br />
Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7090RO:Main Page2008-05-20T05:10:12Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
Taxon A is disjoint from Taxon B<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7089RO:Main Page2008-05-20T05:02:17Z<p>Haendel: /* Since this definition includes 'descended_from', we've been discussing the following more extensive definition: */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of some A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7088RO:Main Page2008-05-20T05:01:29Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is the most recent common ancestor of some A and some B<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Fabian_develops_from.pdf&diff=7085File:Fabian develops from.pdf2008-05-19T21:16:31Z<p>Haendel: </p>
<hr />
<div></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7084OntologyRelations2008-05-19T21:14:42Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Media:Fabian developmental relations.pdf]]<br />
<br />
[[Media:Fabian develops_from.pdf]]<br />
<br />
[[Media:melissa development examples.ppt]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Fabian_developmental_relations.pdf&diff=7082File:Fabian developmental relations.pdf2008-05-19T20:59:35Z<p>Haendel: </p>
<hr />
<div></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7081OntologyRelations2008-05-19T20:58:57Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Media:Fabian developmental relations.pdf]]<br />
<br />
[[Media:melissa development examples.ppt]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Melissa_development_examples.ppt&diff=7080File:Melissa development examples.ppt2008-05-19T20:58:16Z<p>Haendel: </p>
<hr />
<div></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7079OntologyRelations2008-05-19T20:57:42Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Fabian developmental relations.pdf]]<br />
<br />
[[Media:melissa development examples.ppt]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Melissa.Anatomy.examples.ppt&diff=7078File:Melissa.Anatomy.examples.ppt2008-05-19T20:52:19Z<p>Haendel: </p>
<hr />
<div></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7077OntologyRelations2008-05-19T20:50:27Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Fabian developmental relations.pdf]]<br />
<br />
[[Media:melissa development examples]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7076OntologyRelations2008-05-19T20:47:37Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Document:Fabian developmental relations.pdf]]<br />
<br />
[[Media:melissa development examples]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7075OntologyRelations2008-05-19T20:46:18Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Fabian developmental relations.pdf]]<br />
<br />
[[Media:melissa development examples]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7074OntologyRelations2008-05-19T20:44:37Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Media:Fabian developmental relations]]<br />
<br />
[[Media:melissa development examples]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7073OntologyRelations2008-05-19T20:43:54Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
[[Fabian developmental relations]]<br />
<br />
[[melissa development examples]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Dahdul-ROmeeting.ppt&diff=7072File:Dahdul-ROmeeting.ppt2008-05-19T18:56:41Z<p>Haendel: </p>
<hr />
<div></div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7071OntologyRelations2008-05-19T18:55:44Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
[[Media:dahdul-ROmeeting.ppt]]<br />
<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=File:Overlaps.ppt&diff=7070File:Overlaps.ppt2008-05-19T18:44:50Z<p>Haendel: PowerPoints for afternoon of Monday 19 may</p>
<hr />
<div>PowerPoints for afternoon of Monday 19 may</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7068OntologyRelations2008-05-19T18:43:19Z<p>Haendel: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
[[OntologyRelationsMay19MeetingNotes]]<br />
<br />
[[Media:david_sutherland.ppt]]<br />
<br />
[[Media:regulates.ppt]]<br />
<br />
[[Media:overlaps.ppt]]<br />
<br />
[[Media:RO-denver-cjm.ppt]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7046OntologyRelations2008-05-19T04:54:51Z<p>Haendel: /* 2:45 - 4pm: Spatial relations (Melissa/Suzi) */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7045OntologyRelations2008-05-19T04:35:57Z<p>Haendel: /* 2:45 - 4pm: Spatial relations (Melissa/Suzi) */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* Overview and RCC8 (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7044OntologyRelations2008-05-19T04:34:45Z<p>Haendel: /* 10:45am - 12:00 noon: Development and anatomy (DavidOS) */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* Overview and RCC8 (Melissa)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
**Example: tooth attachment use case (bona fide)<br />
* surrounded_by (Chris)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].<br />
<br />
* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7043RO:Main Page2008-05-19T03:49:56Z<p>Haendel: /* Since this definition includes 'descended_from', we've been discussing the following more extensive definition: */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is part of an organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of an organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S sufficient to generate continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is part of an organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of an organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7042RO:Main Page2008-05-19T03:47:23Z<p>Haendel: /* Since this definition includes 'descended_from', we've been discussing the following more extensive definition: */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is part of an organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of an organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S pertaining to continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is part of an organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of an organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendelhttps://www.bioontology.org//mediawiki/index.php?title=RO:Main_Page&diff=7041RO:Main Page2008-05-19T03:46:30Z<p>Haendel: /* Proposed homologous_to relation */</p>
<hr />
<div>=RO - OBO Relation Ontology=<br />
<br />
The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]<br />
<br />
You can browse the ontology and get e-mail list details there.<br />
<br />
=Open issues=<br />
<br />
There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]<br />
<br />
Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]<br />
<br />
==Three types of relations==<br />
<br />
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:<br />
<br />
*1. '''instance_of''' holding between an instance and a type<br />
*2. '''part_of''' holding between an instance and an instance<br />
*3. ''part_of'' holding between a type and a type<br />
<br />
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.<br />
<br />
In the original Genome Biology [http://genomebiology.com/2005/6/5/R46 paper] we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.<br />
<br />
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:<br />
<br />
*c '''instance_of''' C '''at''' t - a primitive relation between a continuant instance and a class which it instantiates at a specific time<br />
<br />
*p '''instance_of''' P - a primitive relation between a process instance and a class which it instantiates holding independently of time<br />
<br />
*c '''part_of''' c1 '''at''' t - a primitive relation between two continuant instances and a time at which the one is part of the other<br />
<br />
*p '''part_of''' p1, r '''part_of''' r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)<br />
<br />
*c '''located_in''' r '''at''' t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time<br />
<br />
*r '''adjacent_to''' r1 - a primitive relation of proximity between two continuants<br />
<br />
*t '''earlier''' t1 - a primitive relation between two times<br />
<br />
*c '''derives_from''' c1 - a primitive relation involving two distinct material continuants c and c1<br />
<br />
*p '''has_participant''' c '''at''' t - a primitive relation between a process, a continuant, and a time<br />
<br />
*p '''has_agent''' c at '''t''' - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process<br />
<br />
In proposing new relations (both on the [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.<br />
<br />
*If it is an instance-level relation, please answer the following questions:<br />
**a. is it already on the list above?<br />
**b. is it primitive in the above-mentioned sense?<br />
*If the answer to both of these questions is no,<br />
**c. can it be defined in terms of the relations on the above list?<br />
*If yes, please supply a definition (an example is provided below)<br />
*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.<br />
<br />
==How to Define an Instance-Level Relation==<br />
<br />
First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).<br />
<br />
All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:<br />
<br />
x is an A =def. x has features F1, F2, F3.<br />
<br />
This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.<br />
<br />
For instance-level relations, the definition might read as follows:<br />
<br />
x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.<br />
<br />
For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).<br />
<br />
With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:<br />
<br />
p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.<br />
<br />
We can then define:<br />
<br />
c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t<br />
<br />
p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t<br />
<br />
:t '''first_instant''' p =def. <br />
::p '''occurring_at''' t, and <br />
::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1<br />
<br />
:t '''last_instant''' p =def. <br />
::p '''occurring_at''' t and <br />
::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1<br />
<br />
:p '''immediately_preceded_by''' p1 =def. <br />
::for some t, t '''first_instant''' p and <br />
::t '''last_instant''' p1.<br />
<br />
In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:<br />
<br />
:p '''has_duration''' y =def. <br />
::p is an occurrent, and<br />
::for some t1, t1 '''first_instant''' p, and<br />
::for some t2, t2 '''last_instant''' p, and<br />
::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps], <br />
;; y is the interval (t1,t2).<br />
<br />
Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.<br />
<br />
==Proposed new type-level relations==<br />
<br />
relations between generically dependent continuants and specifically dependent continuants:<br />
* concretizes<br />
* is_concretized_by<br />
<br />
* about<br />
* inheres_in<br />
* depends_on<br />
* output_of<br />
* has_input<br />
* has_function<br />
* has_quality<br />
* realization_of<br />
* lacks<br />
<br />
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]<br />
<br />
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.<br />
<br />
There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs<br />
<br />
See also <br />
<br />
[http://obofoundry.org/ro/#pending Pending]<br />
<br />
'''The relation of ''overlaps''''' <br />
<br />
X ''overlaps'' Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)<br />
<br />
where <br />
<br />
x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z '''part_of''' y '''at t'''<br />
<br />
Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.<br />
<br />
Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)<br />
<br />
Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.<br />
<br />
==Proposed Gene Ontology 'Regulates' Relations==<br />
<br />
<br />
<br />
[Typedef]<br />
id: OBO_REL:regulates<br />
name: regulates<br />
def: "A relation between a process and a process or quality. A regulates B<br />
if the unfolding of A affects the frequency, rate or extent of B. A is<br />
called the regulating process, B the regulates process" []<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:positively_regulates<br />
name: positively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *increases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
[Typedef]<br />
id: OBO_REL:negatively_regulates<br />
name: negatively_regulates<br />
def: "A regulation relation in which the unfolding of the regulating<br />
process *decreases* the frequency, rate or extent of the regulated process"<br />
[]<br />
is_a: OBO_REL:regulates<br />
transitive_over: OBO_REL:part_of<br />
<br />
Example file:<br />
ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela<br />
tions_test.obo<br />
<br />
Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:<br />
<br />
==Hunter/Bada Proposal for new relations==<br />
<br />
GRANULARITY/SPECIFICITY<br />
<br />
<br />
We assert that the level of granularity/specifity of the proposed<br />
relations is a central issue that, once resolved, will provide useful<br />
guidelines as to what is needed to capture a piece of knowledge by a<br />
relational link. The examples in this proposal use process terms from<br />
the Gene Ontology, but we believe that this issue applies to other OBOs<br />
as well.<br />
<br />
<br />
We assert that the addition of relations should be primarily guided by<br />
the effort to link OBO terms with other OBO terms, as is being done in<br />
the OBO cross-product project. A composite set of links from a given<br />
more complex OBO terms to more atomic OBO terms will provide the<br />
(hopefully complete) definition of the former. A given link from the<br />
term being defined, employing an RO relation, must unambiguously capture<br />
some piece of knowledge, some part of the definition, of this term. It<br />
is this unambiguous representation of some part of the complete<br />
definition of the term that should determine the specificity of the<br />
relation. This may require the use of a specific relation, but we assert<br />
that it is more important to avoid losing knowledge in the represented<br />
definition than to exclusively use general relations.<br />
<br />
<br />
It is ideal to use general, reusable relations in such definitions<br />
without losing information, and we believe that this is sometimes<br />
possible. For example, for the many GO process terms that use “during”<br />
to specify a process that is taking place within the span of another<br />
process (''e.g.'', “actin filament reorganization during cell cycle”), it is<br />
acceptable to use a standard temporal relation, as no information is<br />
lost by doing so. However, especially in the definitions of processes,<br />
we assert that the unambiguous capture of roles of participants will<br />
require relatively specific relations.<br />
<br />
<br />
There have been efforts to use general relations to denote roles, but<br />
they have been difficult to define (''e.g.'', has_agent, has_patient,<br />
has_central_participant) and/or insufficient to specify the role<br />
(''e.g.'', has_output_participant). If suitably precise general relations<br />
cannot be defined, relatively specific relations are needed. Thus, for<br />
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),<br />
if a general relation to indicate what is growing cannot be suitably<br />
defined, then a specific relation must be created to capture this,<br />
either in the form of a lexically analogous relation (''e.g.'',<br />
results_in_growth_of) or as one that incorporates the template<br />
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,<br />
since most of the growth terms are defined as the increase in size or<br />
mass of an entity). These two approaches by themselves are<br />
computationally synonymous but differ in terms of human comprehension.<br />
The former, while not adding information for human users, can be<br />
straightforwardly formed. The latter, while helpful for human users, can<br />
get unwieldy in the case of complex definitions. For example, the<br />
detection-of-stimulus terms are defined as the series of events in which<br />
a stimulus is received by an entity and converted into a molecular<br />
signal, and<br />
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of<br />
is clearly getting ridiculous.<br />
<br />
<br />
It is also ideal for relations, especially relatively specific ones as<br />
exemplified above, to be formally defined (''i.e.'', in a computationlly<br />
procesable way) in terms of more atomic relations. However, it will be<br />
very difficult to produce formal definitions in terms of more atomic<br />
relations, especially for relatively specific relations. We assert that<br />
the linking of OBO terms to generate cross-products should be a<br />
priority, and this requires the specification of relations (as discussed<br />
above) to link the terms. A requirement for any proposed relation to<br />
have a formal decomposed definition in terms of more atomic relations<br />
would be a significant bottleneck to this process. Just as there is no<br />
requirement for an added OBO term to have a formal definition, there<br />
should be no such requirement for an added OBO relation. We would like<br />
to be clear that we believe it extremely beneficial to have such formal<br />
definitions (and thus efforts should continually be put into creating<br />
such definitions), but this should not be an obstacle to the introduction of<br />
new relations.<br />
<br />
<br />
LEXICAL FORM<br />
<br />
<br />
We propose that each relation should canonically be in the form of a<br />
verb phrase. We assert that this promotes usability in that it<br />
emphasizes the fact that these are relationships between entities.<br />
<br />
==TAIR Relations==<br />
<br />
See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684<br />
<br />
Relations between continuants and occurrents:<br />
<br />
* has (function)<br />
* involved in<br />
* functions as<br />
* required for<br />
* functions in<br />
* has protein modification of type<br />
* contributes to<br />
* is upregulated by<br />
* is downregulated by<br />
<br />
Relations between continuants:<br />
<br />
* located in<br />
* expressed in<br />
* colocalizes with<br />
* is subunit of<br />
* constituent of<br />
* has protein-protein physical interaction with<br />
* has protein-DNA interaction with<br />
* binds to cis-element of<br />
* acts upstream of<br />
* acts downstream of<br />
* expressed during<br />
* protein is modified by<br />
* is regulated by<br />
* represses<br />
<br />
Relations between continuants and qualities (phenotypes in our case):<br />
<br />
* suppresses gene<br />
* enhances gene<br />
* partially enhances gene<br />
* partially suppresses gene<br />
<br />
==Proposed homologous_to relation==<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:<br />
<br />
All instances of continuant X part_of some organism which is part of an organism which is an instance of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of an organism which is an instance of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of an organism which is the most recent common ancestor of taxa A and B. <br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z.<br />
<br />
<br />
<br />
===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===<br />
<br />
Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.<br />
<br />
Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S pertaining to continuant E, to species R which is sufficient to generate continuant D.<br />
<br />
Where:<br />
<br />
All instances of continuant X part_of some organism which is part of taxon A<br />
<br />
All instances of continuant Y part_of some organism which is part of taxon B<br />
<br />
All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B. <br />
<br />
All instances of continuant D part_of some organism which is part of species R<br />
<br />
All instances of continuant E part_of some organism which is part of species S<br />
<br />
X is homologous_to Y<br />
<br />
IF (and only if)<br />
<br />
All instances of X descended_from some instance of Z<br />
<br />
AND<br />
<br />
All instances of Y descended_from some instance of Z<br />
<br />
<br />
Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:<br />
<br />
id: OBO_REL:evolutionarily_derived_from<br />
<br />
name: evolutionarily_derived_from<br />
<br />
def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []<br />
<br />
synonym: "derived_from" RELATED []<br />
<br />
synonym: "descended_from" RELATED []<br />
<br />
synonym: "evolved_from" RELATED []<br />
<br />
is_transitive: true<br />
<br />
==OWL Conversion==<br />
<br />
The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details<br />
<br />
obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language</div>Haendel