OBO Foundry

<!doctype html> <html lang="en"> <head> <title>OBO Foundry</title> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.2.2/dist/css/bootstrap.min.css">  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/themes/prism.css" />  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.9.1/font/bootstrap-icons.css">  <link rel="stylesheet" href="/assets/css/style.css"> <link type="application/atom+xml" rel="alternate" href="http://obofoundry.org/feed.xml" title="The OBO Foundry" /> <style> html, body { height: 100%; } body { display: flex; flex-flow: column; } .footer { margin-top: auto; padding-top: 1em; background-color: #f5f5f5; } </style> </head> <body><nav class="navbar navbar-expand-lg navbar-light bg-light"> <div class="container-fluid"> <a class="navbar-brand" href="/"> <img src="/images/foundrylogo.png" alt="" 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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="row"> <h1> <img alt="logo" src="https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png" style="max-height: 1em" /> Mondo Disease Ontology </h1> <p>A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.</p> </div> <div class="row"> <div class="col-md-8" style="padding-left: 0"> <div class="card" style="margin-bottom: 1.5em;"> <div class="card-body">  <a href="https://ontobee.org/ontology/mondo" class="btn btn-outline-primary" target="_blank" rel="noopener"> OntoBee </a> <a href="http://aber-owl.net/ontology/MONDO" class="btn btn-outline-primary" target="_blank" rel="noopener"> AberOWL </a> <a href="http://www.ebi.ac.uk/ols/ontologies/mondo" class="btn btn-outline-primary" target="_blank" rel="noopener"> OLS </a> <a href="https://bioportal.bioontology.org/ontologies/MONDO" class="btn btn-outline-primary" target="_blank" rel="noopener"> BioPortal </a> <a href="https://monarchinitiative.org/disease/MONDO:0019609" class="btn btn-outline-primary" target="_blank" rel="noopener"> Monarch </a> <a href="https://bioregistry.io/metaregistry/obofoundry/mondo" class="btn btn-outline-primary" target="_blank" rel="noopener"> Bioregistry </a> <p class="card-text"><p>The Mondo Disease Ontology (Mondo) aims to harmonize existing disease terminologies into a coherent ontological representation of diseases. Mondo integrates widely used terminologies such as Online Mendelian Inheritance in Man (OMIM), Orphanet, Experimental Factor Ontology (EFO), Disease Ontology (DOID), ICD 11 (Foundation) and the neoplasm branch of National Cancer Institute Thesaurus (NCIt). Mondo aims to track provenance and attribution for every integrated part of the disease definition to serve a wide range of data integration and cross-terminology analysis use cases.</p> <p>A key part of Mondo is the curation of precise mappings across resources. These mappings are available in two ways:</p> <ul> <li>The official Mondo disease mappings in <a href="https://mapping-commons.github.io/sssom/">SSSOM</a> format: <a href="https://github.com/monarch-initiative/mondo/tree/master/src/ontology/mappings">https://github.com/monarch-initiative/mondo/tree/master/src/ontology/mappings</a></li> <li>As part of the various Mondo release products (both as SKOS mappings and oboInOwl:hasDbXref cross-references).</li> </ul> </p> </div> </div> <div class="card" style="margin-bottom: 1.5em;" id="publications"> <div class="card-header"> Publications </div> <div class="list-group list-group-flush"> <div class="list-group-item"> <a href="https://www.medrxiv.org/content/10.1101/2022.04.13.22273750">Mondo: Unifying diseases for the world, by the world</a> </div> </div> </div> <div class="card" style="margin-bottom: 1.5em;"> <div class="card-header"> Products </div> <table class="table table-striped mb-0"> <tbody> <tr> <td> <a href="https://purl.obolibrary.org/obo/mondo.owl">mondo.owl</a> </td> <td>Mondo OWL edition</td> <td> Complete ontology with merged imports. </td> </tr> <tr> <td> <a href="https://purl.obolibrary.org/obo/mondo.obo">mondo.obo</a> </td> <td>Mondo OBO Format edition</td> <td> OBO serialization of mondo.owl. </td> </tr> <tr> <td> <a href="https://purl.obolibrary.org/obo/mondo.json">mondo.json</a> </td> <td>Mondo JSON edition</td> <td> Obographs serialization of mondo.owl. </td> </tr> <tr> <td> <a href="https://purl.obolibrary.org/obo/mondo/mondo-base.owl">mondo/mondo-base.owl</a> </td> <td>Mondo Base Release</td> <td> The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves </td> </tr> <tr> <td> <a href="https://purl.obolibrary.org/obo/mondo/mondo-simple.owl">mondo/mondo-simple.owl</a> </td> <td>Mondo Simple Release</td> <td> The main ontology classes and their hierarchies, without references to external terms. </td> </tr> </tbody> </table> </div> <div class="card" style="margin-bottom: 1.5em;"> <div class="card-header"> Usages </div> <div class="list-group list-group-flush"> <div class="list-group-item"> <dl class="dl-horizontal" style="margin-bottom: 0"> <dt>User</dt> <dd><a href="https://monarchinitiative.org/">https://monarchinitiative.org/</a></dd> <dt>Description</dt> <dd>Mondo is used by the Monarch Initiative for disease annotations.</dd> <dt>Type</dt> <dd>annotation</dd> <dt>Examples</dt> <dd><a href="https://monarchinitiative.org/phenotype/HP:0001300#disease">Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.</a></dd> <dt>Publications</dt> <dd> <ul style="padding-left: 20px"> <li><a href="https://www.ncbi.nlm.nih.gov/pubmed/27899636">The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species </a></li> </ul> </dd> </dl> </div> <div class="list-group-item"> <dl class="dl-horizontal" style="margin-bottom: 0"> <dt>User</dt> <dd><a href="https://www.clinicalgenome.org/">https://www.clinicalgenome.org/</a></dd> <dt>Description</dt> <dd>Mondo is used by the ClinGen for disease curations.</dd> <dt>Type</dt> <dd>annotation</dd> <dt>Examples</dt> <dd><a href="https://search.clinicalgenome.org/kb/conditions/MONDO:0007947">FBN1 is an autosomal dominant mutation in Marfan syndrome.</a></dd> </dl> </div> <div class="list-group-item"> <dl class="dl-horizontal" style="margin-bottom: 0"> <dt>User</dt> <dd><a href="https://portal.kidsfirstdrc.org/">https://portal.kidsfirstdrc.org/</a></dd> <dt>Description</dt> <dd>Mondo is used by the Kids First Data Resource Portal for disease annotations. Note, a login is needed to access the portal and view the Mondo-curated data.</dd> <dt>Type</dt> <dd>annotation</dd> </dl> </div> <div class="list-group-item"> <dl class="dl-horizontal" style="margin-bottom: 0"> <dt>User</dt> <dd><a href="https://www.ancestry.com/">https://www.ancestry.com/</a></dd> <dt>Description</dt> <dd>Mondo is used by the Ancestory for some disease curations.</dd> <dt>Type</dt> <dd>annotation</dd> <dt>Examples</dt> <dd><a href="https://support.ancestry.com/s/article/Disease-Condition-Catalog-Powered-by-MONDO">Some term names in ancestory.com are curated with Mondo, for ease of use.</a></dd> </dl> </div> <div class="list-group-item"> <dl class="dl-horizontal" style="margin-bottom: 0"> <dt>User</dt> <dd><a href="https://www.humancellatlas.org/">https://www.humancellatlas.org/</a></dd> <dt>Description</dt> <dd>Mondo is used by the Human Cell Atlas for some disease annotations.</dd> <dt>Type</dt> <dd>annotation</dd> <dt>Examples</dt> <dd><a href="https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22organ%22,%22terms%22:%5B%22kidney%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22acoustic%20neuroma%22,%22acute%20kidney%20tubular%20necrosis%22%5D%7D%5D&catalog=dcp1">Disease status specimen is normal, type 2 diabetes mellitus.</a></dd> </dl> </div> </div> </div> </div> <div class="col-md-4" style="padding-right: 0"> <dl class="dl-horizontal" style="margin-left: 0"> <dt> ID Space <span data-toggle="tooltip" title="ID prefix" data-html="true"> </span> </dt> <dd> mondo </dd> <dt>PURL</dt> <dd> <a href="http://purl.obolibrary.org/obo/mondo.owl" >http://purl.obolibrary.org/obo/mondo.owl</a > </dd> <dt>License</dt> <dd> <a href="http://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a> </dd> <dt>Homepage</dt> <dd> <a href="https://monarch-initiative.github.io/mondo">https://monarch-initiative.github.io/mondo</a> </dd> <dt>Contact</dt> <dd> <a href="mailto:nicole@tislab.org">Nicole Vasilevsky</a> </dd> <dd> <a href="https://orcid.org/0000-0001-5208-3432">0000-0001-5208-3432</a> </dd> <dd> <a href="https://github.com/nicolevasilevsky">@nicolevasilevsky</a> </dd> <dt>Repository</dt> <dd> <a href="https://github.com/monarch-initiative/mondo">https://github.com/monarch-initiative/mondo</a> </dd> <dt>Tracker</dt> <dd> <a href="https://github.com/monarch-initiative/mondo/issues">https://github.com/monarch-initiative/mondo/issues</a> </dd> <dt>Domain</dt> <dd> health </dd> <dt>Mailing List</dt> <dd> <a href="https://groups.google.com/group/mondo-users">https://groups.google.com/group/mondo-users</a> </dd> <dt>Taxon</dt> <dd> <a href="http://amigo.geneontology.org/amigo/term/NCBITaxon:33208" >Metazoa</a > </dd> <dt>Stars</dt> <dd> <a href="https://github.com/monarch-initiative/mondo"> <img alt="GitHub Repo stars" src="https://img.shields.io/github/stars/monarch-initiative/mondo" /> </a> </dd> <dt>Contributors</dt> <dd> <a href="https://github.com/monarch-initiative/mondo"> <img alt="GitHub contributors" src="https://img.shields.io/github/contributors/monarch-initiative/mondo" /> </a> </dd> <dt>Last Commit</dt> <dd> <a href="https://github.com/monarch-initiative/mondo"> <img alt="GitHub last commit" src="https://img.shields.io/github/last-commit/monarch-initiative/mondo" /> </a>  </dd> </dd> <dt>OBO Dashboard</dt> <dd> <a href="http://dashboard.obofoundry.org/dashboard/mondo/dashboard.html"> <img src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2Fmondo%2Fdashboard-qc-badge.json" alt="OBO Dashboard badge for mondo"/> </a> </dd> </dl> <div class="btn-group pull-right" role="group" aria-label="Source"> <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/mondo.md" class="btn btn-outline-primary" data-toggle="tooltip" title="See FAQ entry: How is metadata stored?" data-html="true" > View </a> <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mondo.md" type="button" data-toggle="tooltip" title="See FAQ entry: How I do edit my metadata?" data-html="true" class="btn btn-outline-primary" > Edit </a> <a href="https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/mondo.yml" data-toggle="tooltip" title="See FAQ entry: How I do edit my PURL?" data-html="true" class="btn btn-outline-primary" > PURL Config </a> </div> <div> Generated by: <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/_layouts/ontology_detail.html" >_layouts/ontology_detail.html</a ><br /> See <a href="/faq/how-do-i-edit-metadata.html">metadata guide</a> </div> </div> </div> </div><footer class="footer"> <p class="small text-center text-muted"> 漏 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 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