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<!DOCTYPE html> <html class="client-nojs" lang="en" dir="ltr"> <head> <meta charset="UTF-8"/> <title>BioPortal FAQ - NCBO Wiki</title> <script>document.documentElement.className="client-js";RLCONF={"wgBreakFrames":!1,"wgSeparatorTransformTable":["",""],"wgDigitTransformTable":["",""],"wgDefaultDateFormat":"dmy","wgMonthNames":["","January","February","March","April","May","June","July","August","September","October","November","December"],"wgRequestId":"cc3bec34c99264c229b46c7c","wgCSPNonce":!1,"wgCanonicalNamespace":"","wgCanonicalSpecialPageName":!1,"wgNamespaceNumber":0,"wgPageName":"BioPortal_FAQ","wgTitle":"BioPortal FAQ","wgCurRevisionId":13061,"wgRevisionId":13061,"wgArticleId":2186,"wgIsArticle":!0,"wgIsRedirect":!1,"wgAction":"view","wgUserName":null,"wgUserGroups":["*"],"wgCategories":[],"wgPageContentLanguage":"en","wgPageContentModel":"wikitext","wgRelevantPageName":"BioPortal_FAQ","wgRelevantArticleId":2186,"wgIsProbablyEditable":!1,"wgRelevantPageIsProbablyEditable":!1,"wgRestrictionEdit":[],"wgRestrictionMove":[],"wgRedirectedFrom":"NCBO_FAQ","wgInternalRedirectTargetUrl": "/wiki/BioPortal_FAQ"};RLSTATE={"site.styles":"ready","noscript":"ready","user.styles":"ready","user":"ready","user.options":"loading","skins.vector.styles.legacy":"ready","mediawiki.toc.styles":"ready"};RLPAGEMODULES=["mediawiki.action.view.redirect","site","mediawiki.page.startup","mediawiki.page.ready","mediawiki.toc","skins.vector.legacy.js"];</script> <script>(RLQ=window.RLQ||[]).push(function(){mw.loader.implement("user.options@1hzgi",function($,jQuery,require,module){/*@nomin*/mw.user.tokens.set({"patrolToken":"+\\","watchToken":"+\\","csrfToken":"+\\"}); });});</script> <link rel="stylesheet" href="/mediawiki/load.php?lang=en&modules=mediawiki.toc.styles%7Cskins.vector.styles.legacy&only=styles&skin=vector"/> <script async="" src="/mediawiki/load.php?lang=en&modules=startup&only=scripts&raw=1&skin=vector"></script> <meta name="generator" content="MediaWiki 1.35.9"/> <link rel="shortcut icon" href="/favicon.ico"/> <link rel="search" type="application/opensearchdescription+xml" href="/mediawiki/opensearch_desc.php" title="NCBO Wiki (en)"/> <link rel="EditURI" type="application/rsd+xml" href="https://www.bioontology.org//mediawiki/api.php?action=rsd"/> <link rel="alternate" type="application/atom+xml" title="NCBO Wiki Atom feed" href="/mediawiki/index.php?title=Special:RecentChanges&feed=atom"/> <link rel="canonical" href="https://www.bioontology.org//wiki/BioPortal_FAQ"/>  </head> <body class="mediawiki ltr sitedir-ltr mw-hide-empty-elt ns-0 ns-subject page-BioPortal_FAQ rootpage-BioPortal_FAQ skin-vector action-view skin-vector-legacy"> <div id="mw-page-base" class="noprint"></div> <div id="mw-head-base" class="noprint"></div> <div id="content" class="mw-body" role="main"> <a id="top"></a> <div id="siteNotice" class="mw-body-content"></div> <div class="mw-indicators mw-body-content"> </div> <h1 id="firstHeading" class="firstHeading" lang="en">BioPortal FAQ</h1> <div id="bodyContent" class="mw-body-content"> <div id="siteSub" class="noprint">From NCBO Wiki</div> <div id="contentSub"><span class="mw-redirectedfrom">(Redirected from <a href="/mediawiki/index.php?title=NCBO_FAQ&redirect=no" class="mw-redirect" title="NCBO FAQ">NCBO FAQ</a>)</span></div> <div id="contentSub2"></div> <div id="jump-to-nav"></div> <a class="mw-jump-link" href="#mw-head">Jump to navigation</a> <a class="mw-jump-link" href="#searchInput">Jump to search</a> <div id="mw-content-text" lang="en" dir="ltr" class="mw-content-ltr"><div class="mw-parser-output"><p><b>Frequently Asked Questions (FAQ)</b> </p> <div id="toc" class="toc" role="navigation" aria-labelledby="mw-toc-heading"><input type="checkbox" role="button" id="toctogglecheckbox" class="toctogglecheckbox" style="display:none" /><div class="toctitle" lang="en" dir="ltr"><h2 id="mw-toc-heading">Contents</h2><span class="toctogglespan"><label class="toctogglelabel" for="toctogglecheckbox"></label></span></div> <ul> <li class="toclevel-1 tocsection-1"><a href="#General"><span class="tocnumber">1</span> <span class="toctext">General</span></a> <ul> <li class="toclevel-2 tocsection-2"><a href="#What_is_an_ontology.3F"><span class="tocnumber">1.1</span> <span class="toctext">What is an ontology?</span></a></li> <li class="toclevel-2 tocsection-3"><a href="#Where_are_the_ontologies.3F"><span class="tocnumber">1.2</span> <span class="toctext">Where are the ontologies?</span></a> <ul> <li class="toclevel-3 tocsection-4"><a href="#How_do_I_submit_an_ontology.3F"><span class="tocnumber">1.2.1</span> <span class="toctext">How do I submit an ontology?</span></a></li> <li class="toclevel-3 tocsection-5"><a href="#How_do_I_cite_BioPortal.3F"><span class="tocnumber">1.2.2</span> <span class="toctext">How do I cite BioPortal?</span></a></li> </ul> </li> </ul> </li> <li class="toclevel-1 tocsection-6"><a href="#Ontology_Content"><span class="tocnumber">2</span> <span class="toctext">Ontology Content</span></a> <ul> <li class="toclevel-2 tocsection-7"><a href="#Building_Ontologies"><span class="tocnumber">2.1</span> <span class="toctext">Building Ontologies</span></a> <ul> <li class="toclevel-3 tocsection-8"><a href="#How_do_I_go_about_building_an_ontology.3F"><span class="tocnumber">2.1.1</span> <span class="toctext">How do I go about building an ontology?</span></a></li> <li class="toclevel-3 tocsection-9"><a href="#What_is_the_OBO_Foundry.3F"><span class="tocnumber">2.1.2</span> <span class="toctext">What is the OBO Foundry?</span></a></li> </ul> </li> </ul> </li> <li class="toclevel-1 tocsection-10"><a href="#BioPortal_Products"><span class="tocnumber">3</span> <span class="toctext">BioPortal Products</span></a> <ul> <li class="toclevel-2 tocsection-11"><a href="#What_is_BioPortal.3F"><span class="tocnumber">3.1</span> <span class="toctext">What is BioPortal?</span></a></li> <li class="toclevel-2 tocsection-12"><a href="#What_is_the_Resource_Index.3F"><span class="tocnumber">3.2</span> <span class="toctext">What is the Resource Index?</span></a></li> <li class="toclevel-2 tocsection-13"><a href="#What_is_the_Annotator.3F"><span class="tocnumber">3.3</span> <span class="toctext">What is the Annotator?</span></a></li> <li class="toclevel-2 tocsection-14"><a href="#I_have_a_lot_of_data_to_analyze._How_can_I_use_the_API_to_access_BioPortal_products_efficiently.3F"><span class="tocnumber">3.4</span> <span class="toctext">I have a lot of data to analyze. How can I use the API to access BioPortal products efficiently?</span></a></li> </ul> </li> <li class="toclevel-1 tocsection-15"><a href="#Details"><span class="tocnumber">4</span> <span class="toctext">Details</span></a> <ul> <li class="toclevel-2 tocsection-16"><a href="#Ontology_Metadata"><span class="tocnumber">4.1</span> <span class="toctext">Ontology Metadata</span></a></li> <li class="toclevel-2 tocsection-17"><a href="#OBO_Format"><span class="tocnumber">4.2</span> <span class="toctext">OBO Format</span></a> <ul> <li class="toclevel-3 tocsection-18"><a href="#What_is_OBO_Format.3F"><span class="tocnumber">4.2.1</span> <span class="toctext">What is OBO Format?</span></a></li> <li class="toclevel-3 tocsection-19"><a href="#Can_I_convert_Obo-format_to_OWL.3F"><span class="tocnumber">4.2.2</span> <span class="toctext">Can I convert Obo-format to OWL?</span></a></li> <li class="toclevel-3 tocsection-20"><a href="#Can_I_convert_Obo-format_files_to_Protege-classic.3F"><span class="tocnumber">4.2.3</span> <span class="toctext">Can I convert Obo-format files to Protege-classic?</span></a></li> </ul> </li> </ul> </li> <li class="toclevel-1 tocsection-21"><a href="#Historical_and_Deprecated_FAQs"><span class="tocnumber">5</span> <span class="toctext">Historical and Deprecated FAQs</span></a> <ul> <li class="toclevel-2 tocsection-22"><a href="#NCBO"><span class="tocnumber">5.1</span> <span class="toctext">NCBO</span></a> <ul> <li class="toclevel-3 tocsection-23"><a href="#What_is_NCBO.3F"><span class="tocnumber">5.1.1</span> <span class="toctext">What is NCBO?</span></a></li> </ul> </li> <li class="toclevel-2 tocsection-24"><a href="#What_is_Open_Biomedical_Data.3F"><span class="tocnumber">5.2</span> <span class="toctext">What is Open Biomedical Data?</span></a></li> <li class="toclevel-2 tocsection-25"><a href="#incomplete_is-a_paths"><span class="tocnumber">5.3</span> <span class="toctext">incomplete is-a paths</span></a> <ul> <li class="toclevel-3 tocsection-26"><a href="#Is_OBO_Format_different_from_the_old_GO_format.3F"><span class="tocnumber">5.3.1</span> <span class="toctext">Is OBO Format different from the old GO format?</span></a></li> <li class="toclevel-3 tocsection-27"><a href="#Where_can_I_find_the_spec.3F"><span class="tocnumber">5.3.2</span> <span class="toctext">Where can I find the spec?</span></a></li> <li class="toclevel-3 tocsection-28"><a href="#Why_not_use_XML.3F"><span class="tocnumber">5.3.3</span> <span class="toctext">Why not use XML?</span></a></li> <li class="toclevel-3 tocsection-29"><a href="#Is_there_a_UML_model.3F"><span class="tocnumber">5.3.4</span> <span class="toctext">Is there a UML model?</span></a></li> <li class="toclevel-3 tocsection-30"><a href="#What_tools_support_Obo-Format.3F"><span class="tocnumber">5.3.5</span> <span class="toctext">What tools support Obo-Format?</span></a></li> </ul> </li> <li class="toclevel-2 tocsection-31"><a href="#Using_Protege_with_OBO_ontologies"><span class="tocnumber">5.4</span> <span class="toctext">Using Protege with OBO ontologies</span></a> <ul> <li class="toclevel-3 tocsection-32"><a href="#Can_I_convert_OBO_format_to_OWL"><span class="tocnumber">5.4.1</span> <span class="toctext">Can I convert OBO format to OWL</span></a></li> </ul> </li> </ul> </li> </ul> </div> <h1><span class="mw-headline" id="General">General</span></h1> <h2><span id="What_is_an_ontology?"></span><span class="mw-headline" id="What_is_an_ontology.3F">What is an ontology?</span></h2> <p>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. </p> <h2><span id="Where_are_the_ontologies?"></span><span class="mw-headline" id="Where_are_the_ontologies.3F">Where are the ontologies?</span></h2> <p>Ontologies are available from BioPortal at <a rel="nofollow" class="external free" href="http://bioportal.bioontology.org">http://bioportal.bioontology.org</a>. </p> <h3><span id="How_do_I_submit_an_ontology?"></span><span class="mw-headline" id="How_do_I_submit_an_ontology.3F">How do I submit an ontology?</span></h3> <p>The current protocol is: </p><p>1) Go to BioPortal at <a rel="nofollow" class="external free" href="http://bioportal.bioontology.org">http://bioportal.bioontology.org</a> </p><p>2) If you haven't already, click on the "Register" link in the top right hand corner. </p><p>3) After you have registered as a user, "Sign In" as that user. </p><p>4) Click on the "Browse" tab (or click on the following link: <a rel="nofollow" class="external free" href="http://bioportal.bioontology.org/browse">http://bioportal.bioontology.org/browse</a>) </p><p>5) Click on the "Submit Ontology" button and follow the instructions. </p> <h3><span id="How_do_I_cite_BioPortal?"></span><span class="mw-headline" id="How_do_I_cite_BioPortal.3F">How do I cite BioPortal?</span></h3> <p>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. </p> <h1><span class="mw-headline" id="Ontology_Content">Ontology Content</span></h1> <h2><span class="mw-headline" id="Building_Ontologies">Building Ontologies</span></h2> <h3><span id="How_do_I_go_about_building_an_ontology?"></span><span class="mw-headline" id="How_do_I_go_about_building_an_ontology.3F">How do I go about building an ontology?</span></h3> <p>There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies: </p><p>1) Protege (<a rel="nofollow" class="external free" href="http://protege.stanford.edu/">http://protege.stanford.edu/</a>) - OWL ontologies </p><p>2) OBOEdit (<a rel="nofollow" class="external free" href="http://oboedit.org/">http://oboedit.org/</a>) - OBO ontologies </p> <h3><span id="What_is_the_OBO_Foundry?"></span><span class="mw-headline" id="What_is_the_OBO_Foundry.3F">What is the OBO Foundry?</span></h3> <p>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 <a rel="nofollow" class="external free" href="http://obofoundry.org/">http://obofoundry.org/</a> </p> <h1><span class="mw-headline" id="BioPortal_Products">BioPortal Products</span></h1> <h2><span id="What_is_BioPortal?"></span><span class="mw-headline" id="What_is_BioPortal.3F">What is BioPortal?</span></h2> <p>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: <a rel="nofollow" class="external free" href="http://bioportal.bioontology.org/">http://bioportal.bioontology.org/</a>. 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 <a href="/mediawiki/index.php?title=Using_BioPortal_Technology_In_Your_Project&action=edit&redlink=1" class="new" title="Using BioPortal Technology In Your Project (page does not exist)">Using BioPortal Technology In Your Project</a> </p><p>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 <a rel="nofollow" class="external free" href="https://www.bioontology.org/BioPortal">http://www.bioontology.org/BioPortal</a>. </p> <h2><span id="What_is_the_Resource_Index?"></span><span class="mw-headline" id="What_is_the_Resource_Index.3F">What is the Resource Index?</span></h2> <p>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. </p> <h2><span id="What_is_the_Annotator?"></span><span class="mw-headline" id="What_is_the_Annotator.3F">What is the Annotator?</span></h2> <p>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. </p> <h2><span id="I_have_a_lot_of_data_to_analyze._How_can_I_use_the_API_to_access_BioPortal_products_efficiently?"></span><span class="mw-headline" id="I_have_a_lot_of_data_to_analyze._How_can_I_use_the_API_to_access_BioPortal_products_efficiently.3F">I have a lot of data to analyze. How can I use the API to access BioPortal products efficiently?</span></h2> <p>This <a rel="nofollow" class="external text" href="https://www.bioontology.org/wiki/Annotator_Optimizing_and_Troublehooting">Annotator Optimizing and Troubleshooting page</a> has many tips that apply to many API requests, not just the NCBO Annotator. </p> <h1><span class="mw-headline" id="Details">Details</span></h1> <h2><span class="mw-headline" id="Ontology_Metadata">Ontology Metadata</span></h2> <p>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 (<a rel="nofollow" class="external free" href="http://omv.ontoware.org/">http://omv.ontoware.org/</a>). </p><p>To read more about how OMV is used in BioPortal see <a href="/wiki/BioPortal_Metadata" title="BioPortal Metadata">BioPortal Metadata Requirements</a>. </p><p>An earlier version of BioPortal's metadata ontology is at <a rel="nofollow" class="external autonumber" href="http://bioportal.bioontology.org/virtual/1148">[1]</a>. </p> <h2><span class="mw-headline" id="OBO_Format">OBO Format</span></h2> <p>Questions about the OBO ontology format </p> <h3><span id="What_is_OBO_Format?"></span><span class="mw-headline" id="What_is_OBO_Format.3F">What is OBO Format?</span></h3> <p>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. </p> <h3><span id="Can_I_convert_Obo-format_to_OWL?"></span><span class="mw-headline" id="Can_I_convert_Obo-format_to_OWL.3F">Can I convert Obo-format to OWL?</span></h3> <p>Yes. There are multiple ways to convert ontologies between OWL and OBO format. </p> <ul><li>Using <a rel="nofollow" class="external text" href="https://protege.stanford.edu">Protege</a> (uses the owl-api which is able to open both OWL and OBO format ontologies)</li></ul> <ul><li>Using BioPortal to load the OBO file (imports using the owl-api; current ontology then available as RDF)</li></ul> <ul><li>Using the owl-api directly</li></ul> <ul><li>use ROBOT <a rel="nofollow" class="external free" href="https://robot.obolibrary.org/convert">https://robot.obolibrary.org/convert</a></li></ul> <h3><span id="Can_I_convert_Obo-format_files_to_Protege-classic?"></span><span class="mw-headline" id="Can_I_convert_Obo-format_files_to_Protege-classic.3F">Can I convert Obo-format files to Protege-classic?</span></h3> <p>Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult. </p><p><br /> </p><p><br /> </p> <h1><span class="mw-headline" id="Historical_and_Deprecated_FAQs">Historical and Deprecated FAQs</span></h1> <h2><span class="mw-headline" id="NCBO">NCBO</span></h2> <h3><span id="What_is_NCBO?"></span><span class="mw-headline" id="What_is_NCBO.3F">What is NCBO?</span></h3> <p>The National Center for Biomedical Ontology (<a rel="nofollow" class="external free" href="https://www.bioontology.org">http://www.bioontology.org</a>) 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鈥檚 software and technologies include <a rel="nofollow" class="external text" href="http://bioportal.bioontology.org">BioPortal</a>, Phenote+, the <a href="/wiki/Resource_Index" title="Resource Index">NCBO Resource Index</a>, and the <a href="/wiki/Annotator_Web_service" title="Annotator Web service">NCBO Annotator</a>. 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鈥檚 sfotware to enhance scientific discovery. </p> <h2><span id="What_is_Open_Biomedical_Data?"></span><span class="mw-headline" id="What_is_Open_Biomedical_Data.3F">What is Open Biomedical Data?</span></h2> <p>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. </p> <h2><span class="mw-headline" id="incomplete_is-a_paths">incomplete is-a paths</span></h2> <p>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). </p><p>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. </p><p>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. </p><p>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. </p> <h3><span id="Is_OBO_Format_different_from_the_old_GO_format?"></span><span class="mw-headline" id="Is_OBO_Format_different_from_the_old_GO_format.3F">Is OBO Format different from the old GO format?</span></h3> <p>Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated. </p> <h3><span id="Where_can_I_find_the_spec?"></span><span class="mw-headline" id="Where_can_I_find_the_spec.3F">Where can I find the spec?</span></h3> <p>You can find details on the 1.0 spec on the GO home page <a rel="nofollow" class="external free" href="http://www.geneontology.org/GO.format.shtml#oboflat">http://www.geneontology.org/GO.format.shtml#oboflat</a> </p><p>This spec is somewhat underspecified </p><p>The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006 </p><p>You can find a preliminary version of the spec here: HTML -- <a rel="nofollow" class="external free" href="http://www.godatabase.org/dev/doc/obo_format_spec.html">http://www.godatabase.org/dev/doc/obo_format_spec.html</a> PDF -- <a rel="nofollow" class="external free" href="http://www.godatabase.org/dev/doc/obo_format_spec.pdf">http://www.godatabase.org/dev/doc/obo_format_spec.pdf</a> Ascii text -- <a rel="nofollow" class="external free" href="http://www.godatabase.org/dev/doc/obo_format_spec.txt">http://www.godatabase.org/dev/doc/obo_format_spec.txt</a> </p> <h3><span id="Why_not_use_XML?"></span><span class="mw-headline" id="Why_not_use_XML.3F">Why not use XML?</span></h3> <p>There is also an obo-xml format. See </p><p><a rel="nofollow" class="external free" href="http://www.godatabase.org/dev/xml">http://www.godatabase.org/dev/xml</a> </p><p>Currently only available as DTD. Relax-NG and XSD coming soon. </p> <h3><span id="Is_there_a_UML_model?"></span><span class="mw-headline" id="Is_there_a_UML_model.3F">Is there a UML model?</span></h3> <p>Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see: </p><p><a rel="nofollow" class="external free" href="http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/">http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/</a> </p> <h3><span id="What_tools_support_Obo-Format?"></span><span class="mw-headline" id="What_tools_support_Obo-Format.3F">What tools support Obo-Format?</span></h3> <p>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 <a rel="nofollow" class="external free" href="http://www.geneontology.org/GO.tools.shtml">http://www.geneontology.org/GO.tools.shtml</a> for a list </p> <dl><dt>OBO-Edit</dt> <dd>(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.</dd></dl> <dl><dt>COBRA</dt> <dd>developed by Stuart Aitken as part of <a rel="nofollow" class="external free" href="http://www.xspan.org">http://www.xspan.org</a>. COBRA is a java ontology editor/viewer for aligning ontologies</dd></dl> <dl><dt>go-perl</dt> <dd><a rel="nofollow" class="external free" href="http://search.cpan.org/~cmungall/go-perl">http://search.cpan.org/~cmungall/go-perl</a></dd></dl> <h2><span class="mw-headline" id="Using_Protege_with_OBO_ontologies">Using Protege with OBO ontologies</span></h2> <p>You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands. </p><p>The OBO plugin was developed at the University of Washington, and is no longer supported. </p><p>You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry. </p><p>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. </p> <h3><span class="mw-headline" id="Can_I_convert_OBO_format_to_OWL">Can I convert OBO format to OWL</span></h3> <ul><li>Using the xslts included in go-perl. <ul><li>Download and install: <a rel="nofollow" class="external free" href="http://search.cpan.org/~cmungall/go-perl/">http://search.cpan.org/~cmungall/go-perl/</a></li> <li>Then run the script</li> <li>go2owl myontology.obo. This functionality will soon be available from oboedit</li> <li>For more details on the mapping, see: <a rel="nofollow" class="external free" href="http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html">http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html</a></li></ul></li></ul>    </div></div><div class="printfooter">Retrieved from "<a dir="ltr" href="https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&oldid=13061">https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&oldid=13061</a>"</div> <div id="catlinks" class="catlinks catlinks-allhidden" data-mw="interface"></div> </div> </div> <div id="mw-navigation"> <h2>Navigation menu</h2> <div id="mw-head">  <nav id="p-personal" class="vector-menu" aria-labelledby="p-personal-label" role="navigation" > <h3 id="p-personal-label"> <span>Personal tools</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="pt-login"><a href="/mediawiki/index.php?title=Special:UserLogin&returnto=BioPortal+FAQ" title="You are encouraged to log in; however, it is not mandatory [o]" accesskey="o">Log in</a></li></ul> </div> </nav> <div id="left-navigation">  <nav id="p-namespaces" class="vector-menu vector-menu-tabs vectorTabs" aria-labelledby="p-namespaces-label" role="navigation" > <h3 id="p-namespaces-label"> <span>Namespaces</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="ca-nstab-main" class="selected"><a href="/wiki/BioPortal_FAQ" title="View the content page [c]" accesskey="c">Page</a></li><li id="ca-talk" class="new"><a href="/mediawiki/index.php?title=Talk:BioPortal_FAQ&action=edit&redlink=1" rel="discussion" title="Discussion about the content page (page does not exist) [t]" accesskey="t">Discussion</a></li></ul> </div> </nav>  <nav id="p-variants" class="vector-menu-empty emptyPortlet vector-menu vector-menu-dropdown vectorMenu" aria-labelledby="p-variants-label" role="navigation" > <input type="checkbox" class="vector-menu-checkbox vectorMenuCheckbox" aria-labelledby="p-variants-label" /> <h3 id="p-variants-label"> <span>Variants</span> </h3>  <div class="body vector-menu-content">  <ul class="menu vector-menu-content-list"></ul> </div> </nav> </div> <div id="right-navigation">  <nav id="p-views" class="vector-menu vector-menu-tabs vectorTabs" aria-labelledby="p-views-label" role="navigation" > <h3 id="p-views-label"> <span>Views</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="ca-view" class="collapsible selected"><a href="/wiki/BioPortal_FAQ">Read</a></li><li id="ca-viewsource" class="collapsible"><a href="/mediawiki/index.php?title=BioPortal_FAQ&action=edit" title="This page is protected.
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