ontology_detail.html

---
layout: default
---

<div class="row">
  <h1>
    {% if page.depicted_by %}
    <img alt="logo" src="{{page.depicted_by}}" style="max-height: 1em" />
    {% endif %} {{ page.title }}
  </h1>
  <p>{{page.description}}</p>
</div>

{% if page.is_obsolete %}
<div class="row">
  <div class="alert alert-danger" role="alert">
    This ontology is deprecated!
  </div>
  {% for repl in page.replaced_by %}
  <div class="alert alert-info" role="alert">
    Consider using: <a href="{{repl}}.html">{{repl}}</a>
  </div>
  {% endfor %}
</div>
{% endif %} {% if page.activity_status == "inactive" %}{% unless
page.is_obsolete %}
<div class="row">
  <div class="alert alert-warning" role="alert">
    This ontology is inactive. For more information see
    <a href="/docs/OntologyStatus.html">here</a>.
  </div>
</div>
{% endunless %}{% endif %} {% if page.activity_status == "orphaned" %}{% unless
page.is_obsolete %}
<div class="row">
  <div class="alert alert-warning" role="alert">
    This ontology is orphaned. For more information see
    <a href="/docs/OntologyStatus.html">here</a>.
  </div>
</div>
{% endunless %}{% endif %} {% if page.preferredPrefix %} {% assign upperPrefix =
page.preferredPrefix | upcase %} {% if upperPrefix != page.preferredPrefix %}
<div class="row">
  <div class="alert alert-info" role="alert">
    This ontology uses a mixed-case prefix. Identifiers and URIs should use: "{{
    page.preferredPrefix }}".
  </div>
</div>
{% endif %} {% endif %}

<div class="row">
  <div class="col-md-8" style="padding-left: 0">
    {% assign stripped_content_size = content | strip | size %}

    <div class="card" style="margin-bottom: 1.5em;">
      <div class="card-body">
        <!-- TODO: each ontology should configure which browsers to be exposed in -->
        <a href="https://ontobee.org/ontology/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
          OntoBee
        </a>
        {% if page.aberowl_id %}
          <a href="http://aber-owl.net/ontology/{{page.aberowl_id | upcase}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
            AberOWL
          </a>
        {% else %}
          <a href="http://aber-owl.net/ontology/{{page.id | upcase}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
            AberOWL
          </a>
        {% endif %}
        <a href="http://www.ebi.ac.uk/ols/ontologies/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
          OLS
        </a>
        {% assign skip_bioportal = false %}
        {% for browser in page.browsers %}
          {% if browser.label == "BioPortal" %}
            {% assign skip_bioportal = true %}
          {% endif %}
        {% endfor %}

        {% unless skip_bioportal %}
          {% assign bioportal_id = page.id | upcase %}
          {% if bioportal_id == 'FBBT' %}
            {% assign bioportal_id = 'FB-BT' %}
          {% elsif bioportal_id == 'RO' %}
            {% assign bioportal_id = 'OBOREL' %}
          {% elsif bioportal_id == 'APOLLO_SV' %}
            {% assign bioportal_id = 'APOLLO-SV' %}
          {% elsif bioportal_id == 'TRANS' %}
            {% assign bioportal_id = 'PTRANS' %}
          {% elsif bioportal_id == 'WBLS' %}
            {% assign bioportal_id = 'WB-LS' %}
          {% elsif bioportal_id == 'FBDV' %}
            {% assign bioportal_id = 'FB-DV' %}
          {% elsif bioportal_id == 'WBBT' %}
            {% assign bioportal_id = 'WB-BT' %}
          {% elsif bioportal_id == 'WBPHENOTYPE' %}
            {% assign bioportal_id = 'WB-PHENOTYPE' %}
          {% elsif bioportal_id == 'TO' %}
            {% assign bioportal_id = 'PTO' %}
          {% elsif bioportal_id == 'FBCV' %}
            {% assign bioportal_id = 'FB-CV' %}
          {% elsif bioportal_id == 'MOD' %}
            {% assign bioportal_id = 'PSIMOD' %}
          {% elsif bioportal_id == 'PSO' %}
            {% assign bioportal_id = 'PLANTSO' %}
          {% endif %}
          <a href="https://bioportal.bioontology.org/ontologies/{{ bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
            BioPortal
          </a>
        {% endunless %}
        {% for b in page.browsers %}
          <a href="{{b.url}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
            {{b.label}}
          </a>
        {% endfor %}
        <a href="https://bioregistry.io/metaregistry/obofoundry/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
         Bioregistry
        </a>
        {% if stripped_content_size > 0 %}
          <p class="card-text">{{ content }}</p>
        {% endif %}
      </div>
    </div>

    {% if page.publications and page.publications.size > 0 %}
    <div class="card" style="margin-bottom: 1.5em;" id="publications">
      <div class="card-header">
        Publications
      </div>
      <div class="list-group list-group-flush">
        {% for p in page.publications %}
        <div class="list-group-item">
          <a href="{{p.id}}">{{p.title}}</a>
          {% if p.preferred %}
          <span class="badge">Preferred</span>
          {% endif %}
        </div>
        {% endfor %}
      </div>
    </div>
    {% endif %}

    {% if page.funded_by %}
    <div class="card" style="margin-bottom: 1.5em;">
      <div class="card-header">
        Funding
      </div>
      <div class="list-group list-group-flush">
        {% for p in page.funded_by %}
        <div class="list-group-item">
          <a href="{{ p.id }}">{{ p.title }}</a>
        </div>
        {% endfor %}
      </div>
    </div>
    {% endif %}

    <div class="card" style="margin-bottom: 1.5em;">
      <div class="card-header">
        Products
      </div>
      <table class="table table-striped mb-0">
        <tbody>
          {% for p in page.products %}
          <tr>
            <td>
              <a href="https://purl.obolibrary.org/obo/{{p.id}}">{{p.id}}</a>
            </td>
            <td>{{p.title}}</td>
            <td>
              {{p.description}} {% if p.page %}
              <a href="{{p.page}}"> [page]</a>
              {% endif %}
            </td>
          </tr>
          {% endfor %}
        </tbody>
      </table>
    </div>

    {% if page.usages %}
    <div class="card" style="margin-bottom: 1.5em;">
      <div class="card-header">
        Usages
      </div>
      <div class="list-group list-group-flush">
        {% for p in page.usages %}
        <div class="list-group-item">
          <dl class="dl-horizontal" style="margin-bottom: 0">
            <dt>User</dt>
            <dd><a href="{{p.user}}">{{p.user}}</a></dd>
            <dt>Description</dt>
            <dd>{{p.description}}</dd>
            {% if p.type %}
            <dt>Type</dt>
            <dd>{{p.type}}</dd>
            {% endif %} {% if p.seeAlso %}
            <dt>See also</dt>
            <dd><a href="{{p.seeAlso}}">{{p.seeAlso}}</a></dd>
            {% endif %} {% if p.examples %}
            <dt>Examples</dt>
            {% for example in p.examples %}
            <dd><a href="{{example.url}}">{{example.description}}</a></dd>
            {% endfor %} {% endif %} {% if p.publications %}
            <dt>Publications</dt>
            <dd>
              <ul style="padding-left: 20px">
                {% for publication in p.publications %}
                <li><a href="{{publication.id}}">{{publication.title}}</a></li>
                {% endfor %}
              </ul>
            </dd>
            {% endif %}
          </dl>
        </div>
        {% endfor %}
      </div>
    </div>
    {% endif %}
  </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>
        {{page.id}}
      </dd>

      <dt>PURL</dt>
      <dd>
        <a href="http://purl.obolibrary.org/obo/{{page.id}}.owl"
          >http://purl.obolibrary.org/obo/{{page.id}}.owl</a
        >
      </dd>

      <dt>License</dt>
      <dd>
        {% if page.license %}
        <a href="{{page.license.url}}">{{page.license.label}}</a>
        {% if page.license.alert %}
        <div class="alert alert-danger" role="alert">
          <span
            class="glyphicon glyphicon-exclamation-sign"
            aria-hidden="true"
          ></span>
          <span class="sr-only">Warning:</span>
          {{page.license.alert}}
        </div>
        {% endif %} {% else %}
        <div class="alert alert-danger" role="alert">
          <span
            class="glyphicon glyphicon-exclamation-sign"
            aria-hidden="true"
          ></span>
          <span class="sr-only">Warning:</span>
          Not entered
        </div>
        {% endif %}
      </dd>

      <dt>Homepage</dt>
      <dd>
        <a href="{{page.homepage}}">{{page.homepage}}</a>
      </dd>
      {% for p in page.page %}
      <dd>
        <a href="{{p}}">{{p}}</a>
      </dd>
      {% endfor %} {% if page.biosharing %}
      <dd>
        <a href="{{page.biosharing}}">{{page.biosharing}}</a>
      </dd>
      {% endif %}

      <dt>Contact</dt>
      <dd>
        <a href="mailto:{{page.contact.email}}">{{page.contact.label}}</a>
      </dd>
      {% if page.contact.orcid %}
      <dd>
        <a href="https://orcid.org/{{ page.contact.orcid }}">{{ page.contact.orcid }}</a>
      </dd>
      {% endif %}
      {% if page.contact.github %}
      <dd>
        <a href="https://github.com/{{ page.contact.github }}">@{{ page.contact.github }}</a>
      </dd>
      {% endif %}

      {% if page.repository and page.repository != page.homepage %}
      <dt>Repository</dt>
      <dd>
        <a href="{{page.repository}}">{{page.repository}}</a>
      </dd>
      {% endif %}

      <dt>Tracker</dt>
      <dd>
        <a href="{{page.tracker}}">{{page.tracker}}</a>
      </dd>

      <dt>Domain</dt>
      <dd>
        {{page.domain}}
      </dd>

      {% if page.mailing_list %}
      <dt>Mailing List</dt>
      <dd>
        <a href="{{page.mailing_list}}">{{page.mailing_list}}</a>
      </dd>
      {% endif %} {% if page.taxon %}
      <dt>Taxon</dt>
      <dd>
        <a href="http://amigo.geneontology.org/amigo/term/{{page.taxon.id}}"
          >{{page.taxon.label}}</a
        >
      </dd>
      {% endif %} {% if page.exampleClass %}
      <dt>Example</dt>
      <dd>
        <a href="http://purl.obolibrary.org/obo/{{page.exampleClass}}"
          >{{page.exampleClass}}</a
        >
      </dd>
      {% endif %} {% if page.issue_requested %}
      <dt>New Ontology Request</dt>
      <dd>
        <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/{{ page.issue_requested }}">
          #{{ page.issue_requested }}
        </a>
      </dd>
      {% endif %} {% if page.dependencies %}
      <dt>Dependencies</dt>
      {% for x in page.dependencies %}
      <dd>
        <a href="{{x.id}}">{{x.id}}</a>
      </dd>
      {% endfor %} {% endif %} {% if page.jobs %}
      <dt>Jobs</dt>
      {% for p in page.jobs %}
      <dd>
        {% if p.type == "travis-cl" or p.id contains "travis" %}
        <a href="{{p.id}}">
          <img alt="Build Status" src="{{p.id}}.svg?branch=master" />
        </a>
        {% else %}
        <a href="{{p.id}}">{{p.type}}</a>
        {% endif %}
      </dd>
      {% endfor %} {% endif %} {% if page.twitter %}
      <dt>Twitter</dt>
      <dd>
        <a
          href="https://twitter.com/{{ page.twitter }}"
          style="padding: 0.5em 0"
        >
          <img
            alt="Twitter Follow"
            src="https://img.shields.io/twitter/follow/{{ page.twitter }}?style=social"
          />
        </a>
      </dd>
      {% endif %} {% if page.repository and page.repository contains
      "https://github.com/" %}
      <dt>Stars</dt>
      <dd>
        <a href="{{ page.repository }}">
          <img
            alt="GitHub Repo stars"
            src="https://img.shields.io/github/stars/{{ page.repository | remove: 'https://github.com/' }}"
          />
        </a>
      </dd>
      <dt>Contributors</dt>
      <dd>
        <a href="{{ page.repository }}">
          <img
            alt="GitHub contributors"
            src="https://img.shields.io/github/contributors/{{ page.repository | remove: 'https://github.com/' }}"
          />
        </a>
      </dd>
      <dt>Last Commit</dt>
      <dd>
        <a href="{{ page.repository }}">
          <img
            alt="GitHub last commit"
            src="https://img.shields.io/github/last-commit/{{ page.repository | remove: 'https://github.com/' }}"
          />
        </a>
        <!--<img alt="GitHub issues" src="https://img.shields.io/github/issues/{{ page.repository | remove: 'https://github.com/' }}" />-->
      </dd>
      {% endif %} {% if page.review.date and page.review.document %}
      <dt>OBO Review</dt>
      <dd>
        {{page.review.date}}
        <a href="{{page.review.document.link}}"
          >{{page.review.document.label}}</a
        >
      </dd>
      <dd>{% endif %}</dd>
      <dt>OBO Dashboard</dt>
      <dd>
        <a href="http://dashboard.obofoundry.org/dashboard/{{ page.id }}/dashboard.html">
          <img src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2F{{ page.id }}%2Fdashboard-qc-badge.json" alt="OBO Dashboard badge for {{ page.id }}"/>
        </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/{{page.id}}.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/{{page.id}}.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/{{page.id}}.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="{{site.repo_src}}_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>