NCBO Wiki - User contributions [en]

BioPortal FAQ

2022-06-08T01:15:48Z

Cmungall: /* Can I convert Obo-format to OWL? */

'''Frequently Asked Questions (FAQ)'''

=General=

==What is an ontology?==
An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.

==Where are the ontologies?==

Ontologies are available from BioPortal at http://bioportal.bioontology.org.

===How do I submit an ontology?===

The current protocol is:

1) Go to BioPortal at http://bioportal.bioontology.org

2) If you haven't already, click on the "Register" link in the top right hand corner.

3) After you have registered as a user, "Sign In" as that user.

4) Click on the "Browse" tab (or click on the following link: http://bioportal.bioontology.org/browse)

5) Click on the "Submit Ontology" button and follow the instructions.

===How do I cite BioPortal?===
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL,
Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data
resources at the click of a mouse. Nucleic Acids Res. 2009 Jul 1;37(Web Server
issue):W170-3. Epub 2009 May 29. PubMed PMID: 19483092; PubMed Central PMCID:
PMC2703982.

=Ontology Content=

==Building Ontologies==

===How do I go about building an ontology?===

There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:

1) Protege (http://protege.stanford.edu/) - OWL ontologies

2) OBOEdit (http://oboedit.org/) - OBO ontologies

===What is the OBO Foundry?===

A collaborative project, involving a group of OBO ontology developers who have agreed in advance to the adoption of a set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/

=BioPortal Products=

==What is BioPortal?==
A Web-based application for searching, sharing, visualizing, and analyzing a large repository of biomedical ontologies, terminologies, and ontology-based annotations. BioPortal is available at: http://bioportal.bioontology.org/. All content of BioPortal is also accessible via RESTful web services. To learn more about how to use BioPortal technology in your software see the page [[Using_BioPortal_Technology_In_Your_Project|Using BioPortal Technology In Your Project]]

BioPortal allows for mappings between terms, bulk export of mappings, visualization of terms and relationships within ontologies, notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal, please visit http://www.bioontology.org/BioPortal.

==What is the Resource Index?==
A set of ontology-based annotations of biomedical data. These annotations have been generated automatically via the Resource Index workflow. The annotations can be accessed from BioPortal, either from from the All Resources tab to search for term annotations or from the Resource Index tab to browse annotations for an individual term. This tool enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.

==What is the Annotator?==
The Annotator is a text annotation tool that uses mgrep, developed by the University of Michigan, as the entity recognizer and the entire library of BioPortal ontologies as the dictionary of terms. This tool can be accessed from BioPortal and also via programmatic access directly to the Web service.

==I have a lot of data to analyze. How can I use the API to access BioPortal products efficiently?==
This [https://www.bioontology.org/wiki/Annotator_Optimizing_and_Troublehooting Annotator Optimizing and Troubleshooting page] has many tips that apply to many API requests, not just the NCBO Annotator.

=Details=

==Ontology Metadata==
Ontology metadata represented in BioPortal uses the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).

To read more about how OMV is used in BioPortal see [[BioPortal_Metadata|BioPortal Metadata Requirements]].

An earlier version of BioPortal's metadata ontology is at [http://bioportal.bioontology.org/virtual/1148].

==OBO Format==

Questions about the OBO ontology format

===What is OBO Format?===

A format often used in the OBO Foundry to define ontologies. OWL is now being recommended by the OBO Foundry community for creating ontologies because of the greater tooling available, but some ontologies are still maintained in OBO format.

===Can I convert Obo-format to OWL?===

Yes. There are multiple ways to convert ontologies between OWL and OBO format.

* Using [https://protege.stanford.edu Protege] (uses the owl-api which is able to open both OWL and OBO format ontologies)

* Using BioPortal to load the OBO file (imports using the owl-api; current ontology then available as RDF)

* Using the owl-api directly

* use ROBOT https://robot.obolibrary.org/convert

===Can I convert Obo-format files to Protege-classic?===

Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.

=Historical and Deprecated FAQs=

==NCBO==

===What is NCBO?===

The National Center for Biomedical Ontology (http://www.bioontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s software and technologies include [http://bioportal.bioontology.org BioPortal], Phenote+, the [[Resource_Index|NCBO Resource Index]], and the [[Annotator_Web_service|NCBO Annotator]]. Partner technologies include LexGrid, Protege, and Jambalaya. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s sfotware to enhance scientific discovery.

==What is Open Biomedical Data?==
A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.

==incomplete is-a paths==

Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).

This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.

Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.

One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.

===Is OBO Format different from the old GO format?===

Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.

===Where can I find the spec?===

You can find details on the 1.0 spec on the GO home page
http://www.geneontology.org/GO.format.shtml#oboflat

This spec is somewhat underspecified

The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006

You can find a preliminary version of the spec here:
HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html
PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf
Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt

===Why not use XML?===

There is also an obo-xml format. See

http://www.godatabase.org/dev/xml

Currently only available as DTD. Relax-NG and XSD coming soon.

===Is there a UML model?===

Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:

http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/

===What tools support Obo-Format?===

The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list

; OBO-Edit
: (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.

; COBRA
: developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies

; go-perl
: http://search.cpan.org/~cmungall/go-perl

==Using Protege with OBO ontologies==

You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.

The OBO plugin was developed at the University of Washington, and is no longer supported.

You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.

Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.

===Can I convert OBO format to OWL===

*Using the xslts included in go-perl.
**Download and install: http://search.cpan.org/~cmungall/go-perl/
**Then run the script
**go2owl myontology.obo. This functionality will soon be available from oboedit
**For more details on the mapping, see: http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html

BioPortal FAQ

2022-06-08T01:14:22Z

Cmungall: /* What is Phenote? */ removing this as I am not sure it's even possible to install this any more!

'''Frequently Asked Questions (FAQ)'''

=General=

==What is an ontology?==
An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.

==Where are the ontologies?==

Ontologies are available from BioPortal at http://bioportal.bioontology.org.

===How do I submit an ontology?===

The current protocol is:

1) Go to BioPortal at http://bioportal.bioontology.org

2) If you haven't already, click on the "Register" link in the top right hand corner.

3) After you have registered as a user, "Sign In" as that user.

4) Click on the "Browse" tab (or click on the following link: http://bioportal.bioontology.org/browse)

5) Click on the "Submit Ontology" button and follow the instructions.

===How do I cite BioPortal?===
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL,
Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data
resources at the click of a mouse. Nucleic Acids Res. 2009 Jul 1;37(Web Server
issue):W170-3. Epub 2009 May 29. PubMed PMID: 19483092; PubMed Central PMCID:
PMC2703982.

=Ontology Content=

==Building Ontologies==

===How do I go about building an ontology?===

There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:

1) Protege (http://protege.stanford.edu/) - OWL ontologies

2) OBOEdit (http://oboedit.org/) - OBO ontologies

===What is the OBO Foundry?===

A collaborative project, involving a group of OBO ontology developers who have agreed in advance to the adoption of a set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/

=BioPortal Products=

==What is BioPortal?==
A Web-based application for searching, sharing, visualizing, and analyzing a large repository of biomedical ontologies, terminologies, and ontology-based annotations. BioPortal is available at: http://bioportal.bioontology.org/. All content of BioPortal is also accessible via RESTful web services. To learn more about how to use BioPortal technology in your software see the page [[Using_BioPortal_Technology_In_Your_Project|Using BioPortal Technology In Your Project]]

BioPortal allows for mappings between terms, bulk export of mappings, visualization of terms and relationships within ontologies, notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal, please visit http://www.bioontology.org/BioPortal.

==What is the Resource Index?==
A set of ontology-based annotations of biomedical data. These annotations have been generated automatically via the Resource Index workflow. The annotations can be accessed from BioPortal, either from from the All Resources tab to search for term annotations or from the Resource Index tab to browse annotations for an individual term. This tool enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.

==What is the Annotator?==
The Annotator is a text annotation tool that uses mgrep, developed by the University of Michigan, as the entity recognizer and the entire library of BioPortal ontologies as the dictionary of terms. This tool can be accessed from BioPortal and also via programmatic access directly to the Web service.

==I have a lot of data to analyze. How can I use the API to access BioPortal products efficiently?==
This [https://www.bioontology.org/wiki/Annotator_Optimizing_and_Troublehooting Annotator Optimizing and Troubleshooting page] has many tips that apply to many API requests, not just the NCBO Annotator.

=Details=

==Ontology Metadata==
Ontology metadata represented in BioPortal uses the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).

To read more about how OMV is used in BioPortal see [[BioPortal_Metadata|BioPortal Metadata Requirements]].

An earlier version of BioPortal's metadata ontology is at [http://bioportal.bioontology.org/virtual/1148].

==OBO Format==

Questions about the OBO ontology format

===What is OBO Format?===

A format often used in the OBO Foundry to define ontologies. OWL is now being recommended by the OBO Foundry community for creating ontologies because of the greater tooling available, but some ontologies are still maintained in OBO format.

===Can I convert Obo-format to OWL?===

Yes. There are multiple ways to convert ontologies between OWL and OBO format.

* Using [https://protege.stanford.edu Protege] (uses the owl-api which is able to open both OWL and OBO format ontologies)

* Using BioPortal to load the OBO file (imports using the owl-api; current ontology then available as RDF)

* Using the owl-api directly

===Can I convert Obo-format files to Protege-classic?===

Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.

=Historical and Deprecated FAQs=

==NCBO==

===What is NCBO?===

The National Center for Biomedical Ontology (http://www.bioontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s software and technologies include [http://bioportal.bioontology.org BioPortal], Phenote+, the [[Resource_Index|NCBO Resource Index]], and the [[Annotator_Web_service|NCBO Annotator]]. Partner technologies include LexGrid, Protege, and Jambalaya. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s sfotware to enhance scientific discovery.

==What is Open Biomedical Data?==
A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.

==incomplete is-a paths==

Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).

This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.

Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.

One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.

===Is OBO Format different from the old GO format?===

Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.

===Where can I find the spec?===

You can find details on the 1.0 spec on the GO home page
http://www.geneontology.org/GO.format.shtml#oboflat

This spec is somewhat underspecified

The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006

You can find a preliminary version of the spec here:
HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html
PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf
Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt

===Why not use XML?===

There is also an obo-xml format. See

http://www.godatabase.org/dev/xml

Currently only available as DTD. Relax-NG and XSD coming soon.

===Is there a UML model?===

Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:

http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/

===What tools support Obo-Format?===

The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list

; OBO-Edit
: (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.

; COBRA
: developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies

; go-perl
: http://search.cpan.org/~cmungall/go-perl

==Using Protege with OBO ontologies==

You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.

The OBO plugin was developed at the University of Washington, and is no longer supported.

You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.

Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.

===Can I convert OBO format to OWL===

*Using the xslts included in go-perl.
**Download and install: http://search.cpan.org/~cmungall/go-perl/
**Then run the script
**go2owl myontology.obo. This functionality will soon be available from oboedit
**For more details on the mapping, see: http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html

CARO:Main Page

2006-08-07T18:51:17Z

Cmungall: /* Background Material */

=CARO=

Welcome to CARO!

This wiki (hosted on the main NCBO public wiki) will contain information on the new CARO reference ontology of anatomy, combining FMA and model organism anatomical ontologies. How this will be achieved is yet to be decided...

=Resources=

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

- [https://lists.sourceforge.net/lists/listinfo/obo-anatomy OBO Anatomy]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

==Meetings==

http://www.bioontology.org/wiki/index.php/Anatomy_Ontology_Workshop

=Background Material=

This is intended as a source of background reading material primarily for the workshop participants. Please help and add more!

==Relations==

Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall CJ, Neuhaus F, Rector A, Rosse C
Relations in Biomedical Ontologies
Genome Biology, 2005, 6:R46

[http://obo.sourceforge.net/relationship OBO Relations]

See also [[RO:Main_Page]], the main RO wiki

==Fiat Boundaries==

As we're in the business of carving up reality, this paper of Barry's might be useful:

http://wings.buffalo.edu/philosophy/faculty/smith/articles/fiatobjects.pdf

==FMA==

A Reference Ontology for Bioinformatics: "The Foundational Model of Anatomy"
Rosse, Cornelius and Mejino, Jose L V (2003) A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics 36:pp. 478-500

http://sigpubs.biostr.washington.edu/archive/00000135/

Barry Smith, Jose L.V. Mejino Jr., Stefan Schulz, Anand Kumar and Cornelius Rosse, “Anatomical Information Science”, in A. G. Cohn and D. M. Mark (eds.), Spatial Information Theory. Proceedings of COSIT 2005 (Lecture Notes in Computer Science), Berlin/Heidelberg/New York: Springer, 149–164.

http://ontology.buffalo.edu/anatomy_GIS/FMA-AIS.pdf

Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst, and Dirk Siebert, "Functional Anatomy: A Taxonomic Proposal”
Acta Biotheoretica, 53(3), 2005, 153–166.
http://ontology.buffalo.edu/medo/Functional_Anatomy.pdf

also on the static versus dynamic see:

Pierre Grenon, Barry Smith and Louis Goldberg, “Biodynamic Ontology: Applying BFO in the Biomedical Domain”, in D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102 (2004)), Amsterdam: IOS Press, 2004, 20–38.
http://ontology.buffalo.edu/medo/biodynamic.pdf

==Model Organisms==

==SAEL==

==Formal Ontology==

File:Pre-coordination.ppt

2006-08-01T00:06:32Z

Cmungall:

Special:Badtitle/NS200:Main Page

2006-08-01T00:05:48Z

Cmungall: /* Old Material */

=PATO - Phenotype and Trait Ontology=

Welcome to the PATO wiki.

PATO was originally devised for the purposes of post-coordinating phenotype annotations using terms from ontologies such as GO and fly anatomy combined with *attribute* and *value* terms. The scope of PATO has been widened, and it is now intended to serve as a reference ontology of biological qualities in general.

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

==Request tracker==

You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications

- http://sourceforge.net/tracker/?group_id=76834&atid=595654[PATO Request tracker]

When submitting term requests, please remember to include definition according to PATO definition guidelines (below)

==Mail list==

You can subscribe or browse the archives here:

- https://lists.sourceforge.net/lists/listinfo/obo-phenotype[OBO-Phenotype Mail List]

The mail list is for discussion of PATO and phenotype annotation in general

=Content=

==Definition guidelines==

Definitions will be specified in accord with [[OBO Foundry]] principles. Each term definition should refine it's parent (genus) term by providing differentiating characteristics that are both necessary and sufficient to discriminate instances of this term from siblings terms. These definitions are of the form "An X is a G which D"

=Annotation=

==OBD==

[http://www.fruitfly.org/~cjm/obd OBD] (temporary page)

==Formats==

http://www.fruitfly.org/~cjm/obd/formats.html

==Chado==

Chado has a module for representing phenotypic data (under revision)

See the [http://www.gmod.org/chado GMOD/Chado page]

=Related ontologies=

PATO is intended to be used with post-coordinated annotations. There are various ontologies containing pre-coordinated phenotype terms. See for example the plant_trait ontology or the mammaliam phenotype [[MP:Main_Page]] ontology

=Old Material=

Primarily for internal NCBO software team reference

*[[Phenotype Reading List]]

[[Media:Pre-coordination.ppt]]

Special:Badtitle/NS200:Main Page

2006-08-01T00:05:38Z

Cmungall: /* Old Material */

OboInOwl:Main Page

2006-07-26T16:22:01Z

Cmungall: /* OboInOwl */

=OboInOwl=

This wiki is for discussing the mapping between Obo1.2 format and OWL

And you can find the first version of this mapping here:

http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html

We are working on a newer version of this mapping

=Mail Lists=

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest:

[https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=Progress=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

=Overview of [Other] Mapping efforts=

Below is a quick summary of the various OBO to OWL conversion efforts that I am aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[[Image:OBOtoOWL.png]]

RO:Main Page

2006-07-18T02:21:04Z

Cmungall: /* OWL Conversion */

RO:Main Page

2006-07-18T01:58:26Z

Cmungall: /* OWL Conversion */

OboInOwl:Main Page

2006-07-18T01:53:27Z

Cmungall:

=OboInOwl=

This wiki is for discussing the mapping between Obo1.2 format and OWL

And you can find the first version of this mapping here:

http://www.godatabase.org/dev/mapping-obo-to-owl.html

We are working on a newer version of this mapping

=Mail Lists=

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest:

[https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=Progress=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

Main Page

2006-07-18T01:48:28Z

Cmungall: /* Ontology Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Shared Materials]]

*[[Evaluation Activities]]

=== Other NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

*[[OboInOwl:Main_Page]] - Mapping between Obo and OWL

CARO:Main Page

2006-07-15T22:19:00Z

Cmungall: /* FMA */

RO:Main Page

2006-07-14T14:23:15Z

Cmungall: /* Proposed new relations */

=RO - OBO Relation Ontology=

The main RO page is located on sourceforge:

- [http://obo.sourceforge.net/relationship]

You can browse the ontology, get mail list details etc there

=Open issues=

==Proposed new relations==

The lacks family of relations is being discussed

Next we will be examining:

has_function, has_quality, and relations that deal with creation, consumption and development

The derives_from relation has been criticised from an ontological POV (REF?). 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

==OWL Conversion==

The standard GO obo->owl conversion is used. See [[Obo2Owl]] for details

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

Note that obo inverse_of is *not* exported to owl:inverseOf. There is no equivalent of the obo language inverse_of in OWL

In Obo 1.2 semantics, inverse only holds for instances

R obo:inverse_of R' => ( x R y => y R' x), where x and y are instances

It would seem that the following holds for owl:

P owl:inverseOf P' => (X P Y => Y P' X)

(TO BE CHECKED - this is my reading of the owl spec)

This does not follow from the definitions of the OBO relations. In fact we go out of our way to make it clear that this is not intended; eg

testis part_of human holds universally for canonical testes
human has_part testis does not hold universally

See the paper for more details

RO:Main Page

2006-07-14T14:16:41Z

Cmungall: /* OWL Conversion */

=RO - OBO Relation Ontology=

The main RO page is located on sourceforge:

- [http://obo.sourceforge.net/relationship]

You can browse the ontology, get mail list details etc there

=Open issues=

==Proposed new relations==

==OWL Conversion==

The standard GO obo->owl conversion is used. See [[Obo2Owl]] for details

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

Note that obo inverse_of is *not* exported to owl:inverseOf. There is no equivalent of the obo language inverse_of in OWL

In Obo 1.2 semantics, inverse only holds for instances

R obo:inverse_of R' => ( x R y => y R' x), where x and y are instances

It would seem that the following holds for owl:

P owl:inverseOf P' => (X P Y => Y P' X)

(TO BE CHECKED - this is my reading of the owl spec)

This does not follow from the definitions of the OBO relations. In fact we go out of our way to make it clear that this is not intended; eg

testis part_of human holds universally for canonical testes
human has_part testis does not hold universally

See the paper for more details

Main Page

2006-07-12T05:38:03Z

Cmungall: /* Ontology Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Shared Materials]]

*[[Evaluation Activities]]

=== Other NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

Special:Badtitle/NS200:Main Page

2006-07-12T05:33:38Z

Cmungall:

Special:Badtitle/NS200:Main Page

2006-07-12T05:30:37Z

Cmungall:

=PATO - Phenotype and Trait Ontology=

Welcome to the PATO wiki.

PATO was originally devised for the purposes of post-coordinating phenotype annotations using terms from ontologies such as GO and fly anatomy combined with *attribute* and *value* terms. The scope of PATO has been widened, and it is now intended to serve as a reference ontology of biological qualities in general.

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

==Request tracker==

You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications

- http://sourceforge.net/tracker/?group_id=76834&atid=595654[PATO Request tracker]

When submitting term requests, please remember to include definition according to PATO definition guidelines (below)

==Mail list==

You can subscribe or browse the archives here:

- https://lists.sourceforge.net/lists/listinfo/obo-phenotype[OBO-Phenotype Mail List]

The mail list is for discussion of PATO and phenotype annotation in general

=Content=

==Definition guidelines==

Definitions will be specified in accord with [[OBO Foundry]] principles. Each term definition should refine it's parent (genus) term by providing differentiating characteristics that are both necessary and sufficient to discriminate instances of this term from siblings terms. These definitions are of the form "An X is a G which D"

=Annotation=

==OBD==

[http://www.fruitfly.org/~cjm/obd OBD] (temporary page)

==Formats==

http://www.fruitfly.org/~cjm/obd/formats.html

==Chado==

Chado has a module for representing phenotypic data (under revision)

See the [http://www.gmod.org/chado GMOD/Chado page]

=Old Material=

Primarily for internal NCBO software team reference

*[[Phenotype Reading List]]

CL:Main Page

2006-07-12T05:28:17Z

Cmungall:

=CL - OBO Cell Ontology=

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

==Request tracker==

None yet. Do we need one?

Submit requests to the list for now

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

Main Page

2006-07-12T05:23:34Z

Cmungall: /* Ontology Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Shared Materials]]

*[[Evaluation Activities]]

=== Other NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

=== Ontology Development Area ===

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]
and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.

Special:Badtitle/NS200:Main Page

2006-07-12T05:20:55Z

Cmungall: /* Chado */

=PATO - Phenotype and Trait Ontology=

Welcome to the PATO wiki.

PATO was originally devised for the purposes of post-coordinating phenotype annotations using terms from ontologies such as GO and fly anatomy combined with *attribute* and *value* terms. The scope of PATO has been widened, and it is now intended to serve as a reference ontology of biological qualities in general.

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

==Request tracker==

You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications

- http://sourceforge.net/tracker/?group_id=76834&atid=595654[PATO Request tracker]

When submitting term requests, please remember to include definition according to PATO definition guidelines (below)

==Mail list==

You can subscribe or browse the archives here:

- https://lists.sourceforge.net/lists/listinfo/obo-phenotype[OBO-Phenotype Mail List]

The mail list is for discussion of PATO and phenotype annotation in general

=Content=

==Definition guidelines==

=Annotation=

==OBD==

[http://www.fruitfly.org/~cjm/obd OBD] (temporary page)

==Formats==

http://www.fruitfly.org/~cjm/obd/formats.html

==Chado==

Chado has a module for representing phenotypic data (under revision)

See the [http://www.gmod.org/chado GMOD/Chado page]

=Old Material=

Primarily for internal NCBO software team reference

*[[Phenotype Reading List]]

Special:Badtitle/NS200:Main Page

2006-07-12T02:16:57Z

Cmungall:

RO:Main Page

2006-07-12T02:15:23Z

Cmungall:

CARO:Main Page

2006-07-12T01:58:43Z

Cmungall:

CARO:Main Page

2006-07-12T01:52:45Z

Cmungall:

Special:Badtitle/NS200:Main Page

2006-07-12T01:36:26Z

Cmungall:

Special:Badtitle/NS200:Main Page

2006-07-12T01:27:42Z

Cmungall:

=PATO - Phenotype and Trait Ontology=

Welcome to the PATO wiki

=Old Material=

*[[Phenotype Reading List]]

Main Page

2006-07-12T01:26:42Z

Cmungall: /* Ontology Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Shared Materials]]

*[[Evaluation Activities]]

=== Other NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

=== Ontology Development Area ===

*[[PATO:Main_Page]] *PATO* - An ontology of phenotypic qualities

*[[RO:Main_Page]] *RO* - OBO Relations ontology

*[[CARO:Main_Page]] *CARO* - Reference anatomical ontology

Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]
and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.