OBO Foundry

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Newsletter </a> <ul class="dropdown-menu" aria-labelledby="navbarNewsletterDropdown"> <li><a class="dropdown-item" href="/newsletter/2025/01/23/7th-issue-newsletter.html">OBO Foundry Newsletter Issue 7</a></li> <li><a class="dropdown-item" href="/newsletter/2024/10/14/6th-issue-newsletter.html">OBO Foundry Newsletter Issue 6</a></li> <li><a class="dropdown-item" href="/newsletter/2024/06/27/5th-issue-newsletter.html">OBO Foundry Newsletter Issue 5</a></li> <li><a class="dropdown-item" href="/newsletter/2024/03/18/4th-issue-newsletter.html">OBO Foundry Newsletter Issue 4</a></li> <li><a class="dropdown-item" href="/newsletter/2023/12/18/3rd-issue-newsletter.html">OBO Foundry Newsletter Issue 3</a></li> <li><a class="dropdown-item" href="/newsletter/2023/09/15/second-issue-newsletter.html">OBO Foundry Newsletter issue 2</a></li> <li><a class="dropdown-item" href="/newsletter/2023/06/16/inaugural-newsletter.html">Inaugural OBO Foundry Newsletter</a></li> </ul> </li> <li class="nav-item"> <a class="nav-link" href="/faq/index.html">FAQ</a> </li> </ul> </div> </div> </nav> <div class="container" style="margin-top: 2em; margin-bottom: 2em;"> <div class="content"> <div> <div class="page-header"> <h1> Principle: Common Format (principle 2) </h1> <p></p> </div> </div> <div class="col-md-12"> <div class="row"> <div class="col-md-3"> <ul> <li> <a href="fp-000-summary.html">Overview</a> </li> <li> <a href="fp-001-open.html">Open (principle 1)</a> </li> <li> <a href="fp-002-format.html">Common Format (principle 2)</a> </li> <li> <a href="fp-003-uris.html">URI/Identifier Space (principle 3)</a> </li> <li> <a href="fp-004-versioning.html">Versioning (principle 4)</a> </li> <li> <a href="fp-005-delineated-content.html">Scope (principle 5)</a> </li> <li> <a href="fp-006-textual-definitions.html">Textual Definitions (principle 6)</a> </li> <li> <a href="fp-007-relations.html">Relations (principle 7)</a> </li> <li> <a href="fp-008-documented.html">Documentation (principle 8)</a> </li> <li> <a href="fp-009-users.html">Documented Plurality of Users (principle 9)</a> </li> <li> <a href="fp-010-collaboration.html">Commitment To Collaboration (principle 10)</a> </li> <li> <a href="fp-011-locus-of-authority.html">Locus of Authority (principle 11)</a> </li> <li> <a href="fp-012-naming-conventions.html">Naming Conventions (principle 12)</a> </li> <li> <a href="fp-013-notification.html">Notification of Changes (principle 13)</a> </li> <li> <a href="fp-016-maintenance.html">Maintenance (principle 16)</a> </li> <li> <a href="fp-020-responsiveness.html">Responsiveness (principle 20)</a> </li> </ul> <div class="btn-group" role="group" aria-label="Source"> <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/principles/fp-002-format.md" > <button type="button" data-toggle="tooltip" title="See FAQ entry: How I do propose edits to principles?" html="true" class="btn btn-outline-primary" > View </button> </a> <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/principles/fp-002-format.md" > <button type="button" data-toggle="tooltip" title="See FAQ entry: How I do propose edits to principles?" html="true" class="btn btn-outline-primary" > Edit </button> </a>  </div> <div> This page is generated via <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/_layouts/principle.html" >_layouts/principle.html</a >. See <a href="/faq/how-do-i-edit-content.html">edit guide</a> </div> </div> <div class="col-md-9"><p>GO TO: <a href="#recommendations-and-requirements">Recommendations/Requirements</a> | <a href="#implementation">Implementation</a> | <a href="#examples">Examples/Counter‑Examples</a> | <a href="#criteria-for-review">Criteria for Review</a> | <a href="#feedback-and-discussion">Feedback/Discussion</a></p> <h2 id="summary">Summary</h2> <p>The ontology is made available in a common formal language in an accepted concrete syntax.</p> <h2 id="purpose">Purpose</h2> <p>A common format allows the maximum number of people to access and reuse an ontology.</p> <h2 id="recommendations-and-requirements">Recommendations and Requirements</h2> <p>All ontologies MUST have at least one OWL product whose name corresponds to the registered prefix (e.g., ‘GO’ –> go.owl, ‘OBI’ –> obi.owl). Thus the ontology whose IRI is http://purl.obolibrary.org/obo/ro.owl (known to the OBO Foundry as ‘RO’), must have at least the product ro.owl. Developers are free to use whatever combination of technologies and formats is appropriate for development. However, the official OWL PURL (see <a href="https://obofoundry.org/principles/fp-003-uris.html">Principle 3</a>) for the ontology MUST resolve to a syntactically valid OWL file using the <a href="https://www.w3.org/TR/rdf-syntax-grammar/">RDF-XML</a> syntax.</p> <p>Developers can OPTIONALLY produce ontologies in other formats. These are conventionally the same IRI as the owl, but with .owl changed to the relevant extension (e.g., ‘.obo’, ‘.json’). Note that such products are not listed by default. If you produce an additional format product, you should register it under the ‘products’ field in the appropriate metadata file found in this <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology">folder</a>.</p> <h2 id="implementation">Implementation</h2> <p>ROBOT offers functionality to convert a variety of formats, including OBO, to RDF/XML. Protégé allows you to save ontologies in RDF/XML, as well. The <a href="https://ontology101tutorial.readthedocs.io/en/latest/StartingProtege.html">Ontology 101 Tutorial</a> has directions on starting and saving in Protégé.</p> <h2 id="examples">Examples</h2> <ul> <li> <p>The <a href="http://geneontology.org">Gene Ontology</a> is maintained as OBO-Format. It is automatically converted to OWL and is available in both OBO and OWL via the OBO Foundry.</p> </li> <li> <p>The <a href="https://www.ebi.ac.uk/chebi/">ChEBI ontology</a> is maintained in a relational database using a custom schema, but makes an OBO-Format file available that is automatically converted to OWL. It is available in both OBO and OWL via the OBO Foundry.</p> </li> <li> <p><a href="http://obi-ontology.org">OBI</a> is maintained as an OWL ontology.</p> </li> </ul> <h2 id="counter-examples">Counter-Examples</h2> <p>An ontology that is in Frames format, OWL/XML, or OWL Manchester Syntax.</p> <h2 id="criteria-for-review">Criteria for Review</h2> <p>The ontology MUST be available in RDF/XML format.</p> <p><a href="checks/fp_002">This check is automatically validated.</a> The automatic check fully covers the requirements for this principle.</p> <h2 id="feedback-and-discussion">Feedback and Discussion</h2> <p>To suggest revisions or begin a discussion pertaining to this principle, please <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/new?labels=attn%3A+Editorial+WG,principles&title=Principle+%232+%22Format%22+%3CENTER+ISSUE+TITLE%3E">create an issue on GitHub</a>.</p> <p>To suggest revisions or begin a discussion pertaining to the automated validation of this principle, please <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/new?labels=attn%3A+Technical+WG,automated+validation+of+principles&title=Principle+%232+%22Format%22+-+automated+validation+%3CENTER+ISSUE+TITLE%3E">create an issue on GitHub</a>.</p> </div> </div> </div> </div> </div><footer class="footer"> <p class="small text-center text-muted"> © 2024 OBO Technical WG </p> </footer> <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.2.2/dist/js/bootstrap.bundle.min.js"></script>  <script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/prism.min.js"></script> <script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/plugins/autoloader/prism-autoloader.min.js"></script> </body> </html>

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