Difference between revisions of "BioPortal FAQ"

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Frequently Asked Questions within cBio
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'''Frequently Asked Questions (FAQ)'''
  
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This FAQ is currently in alpha - please be patient...
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=General=
  
−
=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.
  
−
==NCBO==
+
===How do I submit an ontology?===
  
−
===What is NCBO?===
+
The current protocol is:
  
−
National Center for Biomedical Ontology
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1) Go to BioPortal at http://bioportal.bioontology.org
  
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==OBO==
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2) If you haven't already, click on the "Register" link in the top right hand corner. 
  
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===What is OBO?===
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3) After you have registered as a user, "Sign In" as that user.
  
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Open Biomedical Ontologies
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4) Click on the "Browse" tab (or click on the following link: http://bioportal.bioontology.org/browse)
  
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===Where are the ontologies?===
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5) Click on the "Submit Ontology" button and follow the instructions.
  
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Currently on http://obo.sourceforge.net
+
===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.
  
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Soon to be moving to the NCBO site
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=Ontology Content=
  
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===How do I submit an ontology?===
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==Building Ontologies==
  
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The current protocol is:
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===How do I go about building an ontology?===
  
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Send an email to the obo-discuss mailing list, even if the ontology is in planning stages
+
There are a plethora of tools for building ontologies.  Below are two preferred tools for building OWL and OBO ontologies:
  
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If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site
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1) Protege (http://protege.stanford.edu/) - OWL ontologies
  
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Soon we will have an ontology submission service on the NCBO website
+
2) OBOEdit (http://oboedit.org/) - OBO ontologies
  
−
=Ontology Content=
+
===What is the OBO Foundry?===
  
−
==Building Ontologies==
+
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/
  
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===How do I go about building an ontology?===
+
=BioPortal Products=
  
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===What is the OBO Gold standard?===
+
==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]]
  
−
==Current Ontologies
+
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.
  
−
===incomplete is-a paths===
+
==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.
  
−
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).
+
==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.
  
−
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.
+
==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.
  
−
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.
+
=Details=
  
−
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.
+
==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/).
  
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=Technical=
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To read more about how OMV is used in BioPortal see [[BioPortal_Metadata|BioPortal Metadata Requirements]].
  
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Questions for cores 1 and 2
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An earlier version of BioPortal's metadata ontology is at [http://bioportal.bioontology.org/virtual/1148].
  
 
==OBO Format==
 
==OBO Format==
  
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Questions about the OBO text and xml formats
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Questions about the OBO ontology format
  
 
===What is OBO 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?===
 
===Is OBO Format different from the old GO format?===
Line 118: Line 176:
 
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.
 
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.
  
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===Can I convert Obo-format to OWL?===
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===Can I convert OBO format to OWL===
−
 
 
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Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.
 
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Download and install:
 
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http://search.cpan.org/~cmungall/go-perl/
 
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Then run the script
 
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  go2owl myontology.obo
 
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This functionality will soon be available from oboedit
 
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For more details on the mapping, see:
 
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http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html
 
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===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===
 
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You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:
 
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http://www.fruitfly.org/~cjm/obo-download
 
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===Can I convert Obo-format files to Protege-classic?===
 
−
 
 
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Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.
 
−
 
 
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==Ontology Metadata==
 
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==OBD==
 
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===What is OBD?===
 
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OBD is a database for storing data typed using OBO ontologies
 
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===Where is it?===
 
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In development!
 
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===Is there a demo?===
 
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See http://www.fruitfly.org/~cjm/obd
 
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===Datasets===
 
  
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See the above URL for now
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*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

Latest revision as of 18:15, 7 June 2022

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

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 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 Requirements.

An earlier version of BioPortal's metadata ontology is at [1].

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 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 BioPortal, Phenote+, the NCBO Resource Index, and the 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

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