https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Mathias 2026-06-05T13:42:18Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6071 2007-09-23T16:07:39Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> <br /> Hi Mathias - agreed, fly, insect and organism should not be siblings. These terms should probably not even be in IDO as they are (i think) in other ontologies. What do others think?<br /> <br /> '''I completely agree.'''<br /> <br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias<br /> <br /> '''Owl file should be there now, along with an OBO Edit file. Dates in filenames indicate which is the most recent. In the near term, we will work in OBO Edit and use the converter to update the OWL file. When we begin asserting relations other than is_a and part_of, we will probably migrate to OWL. We will keep the group informed.'''<br /> <br /> How do you define &quot;pain&quot;. Depending on the definition I would not agree that pain is an object. Mathias<br /> <br /> Good question. We had lots of interesting discussion about pain. Is pain the perception or the signals that the brain receives and perceives as pain? What do you think?<br /> <br /> '''I am rather certain that pain is not an independent contiuant''',''' so it has to go to the dependent branch. Maybe it is a symptom?'''<br /> <br /> I am not sure whether being epidemic and being pandemic qualifies as a criterion differntiating two universals. I'd think this is either two FiatProcessParts (since the thresholds are defied by humans, if I remember that right, or maybe a property or a quality.....What do you think? Mathias<br /> <br /> '''hmmm. i think i need to go reread parts of the BFO manual ...<br /> '''<br /> <br /> '''ps i bolded my responses so they would stand out but feel free to unbold them and bold yours so the new comments standout.'''</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6059 2007-09-20T20:30:53Z

<p>Mathias: </p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> Univ. of Michigan: Vaccine DB<br /> <br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO [http://www.geneontology.org/] (PAMGO [http://pamgo.vbi.vt.edu/], Immune System Process)<br /> <br /> FMA [http://sig.biostr.washington.edu/projects/fm/]<br /> <br /> CARO [http://www.bioontology.org/wiki/index.php/CARO:Main_Page]<br /> <br /> D.O. [http://diseaseontology.sourceforge.net/]<br /> <br /> EnvO [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo]<br /> <br /> ChEBI [http://www.ebi.ac.uk/chebi/]<br /> <br /> PRO [http://pir.georgetown.edu/pro/]<br /> <br /> OBI [http://obi.sourceforge.net/index.php]<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations<br /> <br /> <br /> <br /> == Future plans ==<br /> <br /> Contributions:<br /> <br /> Univ. of Michigan: Brucellosis<br /> <br /> Crete: Vector-born diseases (Malaria)<br /> <br /> CSU: Dengue<br /> <br /> UT Southwestern: Pathogen-related terms<br /> <br /> Cleveland Clinic: Infective endocarditis<br /> <br /> MITRE: Influenza<br /> <br /> Mt. Sinai: Influenza</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6058 2007-09-20T18:51:02Z

<p>Mathias: /* Existing Ontologies */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO [http://www.geneontology.org/] (PAMGO [http://pamgo.vbi.vt.edu/], Immune System Process)<br /> <br /> FMA [http://sig.biostr.washington.edu/projects/fm/]<br /> <br /> CARO [http://www.bioontology.org/wiki/index.php/CARO:Main_Page]<br /> <br /> D.O. [http://diseaseontology.sourceforge.net/]<br /> <br /> EnvO [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo]<br /> <br /> ChEBI [http://www.ebi.ac.uk/chebi/]<br /> <br /> PRO [http://pir.georgetown.edu/pro/]<br /> <br /> OBI [http://obi.sourceforge.net/index.php]<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6057 2007-09-20T16:08:30Z

<p>Mathias: /* Existing Ontologies */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO [http://www.geneontology.org/] (PAMGO [http://pamgo.vbi.vt.edu/], Immune System Process)<br /> <br /> FMA [http://sig.biostr.washington.edu/projects/fm/]<br /> <br /> CARO [http://www.bioontology.org/wiki/index.php/CARO:Main_Page]<br /> <br /> D.O. [http://diseaseontology.sourceforge.net/]<br /> <br /> EnvO [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo]<br /> <br /> ChEBI [http://www.ebi.ac.uk/chebi/]<br /> <br /> PRO [http://pir.georgetown.edu/pro/]<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6055 2007-09-20T15:59:40Z

<p>Mathias: /* Existing Ontologies */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO [http://www.geneontology.org/] (PANGO, Immune System Process)<br /> <br /> FMA [http://sig.biostr.washington.edu/projects/fm/]<br /> <br /> CARO<br /> <br /> D.O. [http://diseaseontology.sourceforge.net/]<br /> <br /> EnvO [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo]<br /> <br /> ChEBI [http://www.ebi.ac.uk/chebi/]<br /> <br /> PRO<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6054 2007-09-20T15:52:22Z

<p>Mathias: /* Existing Ontologies */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO [http://www.geneontology.org/] (PANGO, Immune System Process)<br /> <br /> FMA [http://sig.biostr.washington.edu/projects/fm/]<br /> <br /> CARO<br /> <br /> D.O. [http://diseaseontology.sourceforge.net/]<br /> <br /> EnvO <br /> <br /> ChEBI<br /> <br /> PRO<br /> <br /> Pathogen<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6053 2007-09-20T15:45:36Z

<p>Mathias: /* Data */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Virulence Factor DB<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO (PANGO, Immune System Process)<br /> <br /> FMA<br /> <br /> CARO<br /> <br /> D.O.<br /> <br /> EnvO<br /> <br /> ChEBI<br /> <br /> PRO<br /> <br /> Pathogen<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6052 2007-09-20T15:44:50Z

<p>Mathias: /* Existing Ontologies */</p> <hr /> <div>== Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO (PANGO, Immune System Process)<br /> <br /> FMA<br /> <br /> CARO<br /> <br /> D.O.<br /> <br /> EnvO<br /> <br /> ChEBI<br /> <br /> PRO<br /> <br /> Pathogen<br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Toolbox&diff=6051 2007-09-20T15:43:59Z

<p>Mathias: New page: == Morning session 09/20/07 == == Data == TBDB (TB Data + Microarray) SMD (Stanford Microarray Data) Dengue Case Data Insect/Vector Epidemiological Data (Gates Funded) Proteomics ...</p> <hr /> <div><br /> == Morning session 09/20/07 ==<br /> <br /> <br /> <br /> == Data ==<br /> <br /> TBDB (TB Data + Microarray)<br /> <br /> SMD (Stanford Microarray Data)<br /> <br /> Dengue Case Data<br /> <br /> Insect/Vector Epidemiological Data (Gates Funded)<br /> <br /> Proteomics Data (comparative data on strains of pathogens)<br /> <br /> GOA for plants adn animals (response to other organism)<br /> <br /> Sequence data for Influenza (infected animal)<br /> <br /> NIAID -&gt; PIR<br /> <br /> <br /> == Existing Ontologies ==<br /> <br /> <br /> GO<br /> <br /> (PANGO<br /> <br /> Immune System Process)<br /> <br /> FMA<br /> <br /> CARO<br /> <br /> D.O.<br /> <br /> EnvO<br /> <br /> ChEBI<br /> <br /> PRO<br /> <br /> Pathogen<br /> <br /> <br /> <br /> == Agenda: ==<br /> <br /> <br /> <br /> scope<br /> <br /> term list<br /> <br /> BFO type<br /> <br /> taxonomy<br /> <br /> additional relations</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6050 2007-09-20T15:41:42Z

<p>Mathias: /* News */</p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.19.07.obo<br /> <br /> Accesible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6045 2007-09-19T20:47:56Z

<p>Mathias: /* Recommended Background Reading */</p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here: [[Image:IDO Draft.pdf]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6044 2007-09-19T20:45:37Z

<p>Mathias: </p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here: [[Image:IDO Draft.pdf]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see [[http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]]<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6037 2007-09-19T17:48:05Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> <br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias<br /> <br /> How do you define &quot;pain&quot;. Depending on the definition I would not agree that pain is an object. Mathias<br /> <br /> I am not sure whether being epidemic and being pandemic qualifies as a criterion differntiating two universals. I'd think this is either two FiatProcessParts (since the thresholds are defied by humans, if I remember that right, or maybe a property or a quality.....What do you think? Mathias</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6034 2007-09-19T17:42:12Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> <br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias<br /> <br /> How do you define &quot;pain&quot;. Depending on the definition I would not agree that pain is an object. Mathias</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6033 2007-09-19T17:41:52Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias<br /> How do you define &quot;pain&quot;. Depending on the definition I would not agree that pain is an object. Mathias</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6032 2007-09-18T01:55:22Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6031 2007-09-18T01:52:35Z

<p>Mathias: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)</div>

Mathias https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6030 2007-09-18T01:52:08Z

<p>Mathias: New page: I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this?</p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this?</div>

Mathias