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fix: clean up citations section + associated language (#2610)
* fix: clean up some language regarding citations * additional work * Tweak wording
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‎_includes/citation_toc.md‎

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[OBO Citation and Attribution Policy](/citation/Citation.html)
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- [Referring to a single term](/citation/Citation.html#single-term)
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- [Referring to an ontology](/citation/Citation.html#refer-ontology)
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- [Citing an ontology](/citation/Citation.html#cite-ontology)
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[OBO Foundry Publications](/citation/RelatedPublications.html)
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- [Citing the OBO Foundry](/citation/RelatedPublications.html#citing)
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- [Other OBO Foundry Publications](/citation/RelatedPublications.html#other)
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[OBO Foundry Ontology Publications](/citation/KnownPublications.html)

‎_includes/header.html‎

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Citation
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</a>
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<ul class="dropdown-menu" aria-labelledby="navbarCitationDropdown">
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<li><a class="dropdown-item" href="/docs/Citation.html">Cite Ontologies</a></li>
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<li><a class="dropdown-item" href="/registry/publications.html">Cite the OBO Foundry</a></li>
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<li><a class="dropdown-item" href="/registry/publications.html">Publications Related to the OBO
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Foundry</a></li>
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<li><a class="dropdown-item" href="/citation/Citation.html">Cite Ontologies</a></li>
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<li><a class="dropdown-item" href="/citation/RelatedPublications.html">OBO Foundry Publications</a></li>
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<li><a class="dropdown-item" href="/citation/KnownPublications.html">Known OBO Foundry Ontology Publications</a></li>
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</ul>
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</li>
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‎_layouts/citation.html‎

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---
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layout: default
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---
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<div class="content">
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<div>
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<div class="page-header">
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<h1>{{ page.title }}</h1>
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</div>
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</div>
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<div class="col-md-12">
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<div class="row">
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<div class="col-md-3">
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{% capture my_include %}{% include citation_toc.md %}{% endcapture %} {{
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my_include | markdownify }} {% if page.id %}
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<div class="btn-group" role="group" aria-label="Source">
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<a
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href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/citation/{{page.id}}.md"
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>
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<button
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type="button"
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data-toggle="tooltip"
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title="See FAQ entry: How is metadata stored?"
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html="true"
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class="btn btn-outline-primary"
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>
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View
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</button>
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</a>
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<a
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href="https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/citation/{{page.id}}.md"
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>
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<button
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type="button"
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data-toggle="tooltip"
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title="See FAQ entry: How I do edit my metadata?"
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html="true"
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class="btn btn-outline-primary"
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>
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Edit
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</button>
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</a>
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<!-- <button type="button" class="btn btn-outline-primary">Help</button> -->
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</div>
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{% endif %}
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</div>
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<div class="col-md-9">{{ content }}</div>
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</div>
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</div>
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</div>
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‎_layouts/ontology_detail.html‎

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</div>
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</div>
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{% if page.publications %}
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<div class="card" style="margin-bottom: 1.5em;">
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{% if page.publications and page.publications.size > 0 %}
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<div class="card" style="margin-bottom: 1.5em;" id="publications">
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<div class="card-header">
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Publications
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</div>

‎assets/css/style.css‎

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.dash-status {
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margin-bottom: 3px;
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}
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/*
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Custom blockquote formatting
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*/
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.citation-blockquote {
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padding: 5px;
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margin-left: 20px;
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margin-bottom: 16px;
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}

docs/Citation.md renamed to citation/Citation.md

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---
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layout: doc
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layout: citation
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title: OBO Citation and Attribution Policy
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---
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Open Biological and Biomedical Ontologies are used in a diversity of ways. The following guidelines are intended to promote proper attribution of the ontology creators and contributors, and to promote reproducibility in informatics applications.
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Open Biological and Biomedical Ontologies are used in a variety of ways. The following guidelines are intended to promote proper attribution of the ontology creators and contributors, and to promote reproducibility in informatics applications.
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## Referring to a single term
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<h2 id="single-term">Referring to a single term</h2>
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When referring to a single ontology term, use the full [Internationalized Resource Identifier (IRI)](http://tools.ietf.org/html/rfc3987), for example:
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> http://purl.obolibrary.org/obo/UBERON_0000948
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<div class="citation-blockquote">
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http://purl.obolibrary.org/obo/UBERON_0000948
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</div>
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You can use a shorter [Compact URI (CURIE)](https://www.w3.org/TR/curie/) by defining a prefix that abbreviates the first part of the IRI. For example, the prefix "UBERON" can abbreviate "http://purl.obolibrary.org/obo/UBERON_", then "http://purl.obolibrary.org/obo/UBERON_0000948" can be shortened to "[UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948)". A footnote like this one should be included with the first use of the prefix:
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> [UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948) is a Compact URI (CURIE). Here and subsequently the prefix "UBERON" expands to "http://purl.obolibrary.org/obo/UBERON_". The full identifier for the term is then <http://purl.obolibrary.org/obo/UBERON_0000948>. Browsing to this address gives further information about the term.
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<div class="citation-blockquote">
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<a href="http://purl.obolibrary.org/obo/UBERON_0000948">UBERON:0000948</a> is a Compact URI (CURIE). Here and subsequently the prefix "UBERON" expands to "http://purl.obolibrary.org/obo/UBERON_". The full identifier for the term is then <a href="http://purl.obolibrary.org/obo/UBERON_0000948">http://purl.obolibrary.org/obo/UBERON_0000948</a>. Browsing to this address gives further information about the term.
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</div>
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In situations that allow the use of hyperlinks, every CURIE should be a hyperlink with its full IRI as its target, as in these examples.
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We also recommend including the primary label of the term in quotation marks before the IRI or CURIE:
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> 'heart' ([UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948))
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<div class="citation-blockquote">
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'heart' (<a href="http://purl.obolibrary.org/obo/UBERON_0000948">UBERON:0000948</a>)
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</div>
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## Referring to an ontology
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<h2 id="refer-ontology">Referring to an ontology</h2>
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To facilitate reproducibility, be specific about the version of the ontology that you are referring to by using an ontology version IRI that contains the release date:
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> http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl
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<div class="citation-blockquote">
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http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl
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</div>
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The ontology version IRI is indicated by the [owl:versionIRI](https://www.w3.org/2002/07/owl#versionIRI) property.
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When referring to an ontology in general (not a specific version) you can use its ontology IRI:
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> http://purl.obolibrary.org/obo/uberon.owl
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<div class="citation-blockquote">
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http://purl.obolibrary.org/obo/uberon.owl
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</div>
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The ontology IRI or ontology version IRI should be accompanied by a citation of the ontology, in any context where citations are appropriate.
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## Citing an ontology
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<h2 id="cite-ontology">Citing an ontology</h2>
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Some ontologies recommend citation of specific publications. Please see their respective homepages for this information. For example, [Uberon](http://obofoundry.org/ontology/uberon) lists two publications under "Cite."
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Some ontologies recommend citation of specific publications. Please see their respective homepages for this information. For example, [Uberon]({{ "ontology/uberon.html#publications" | prepend: site.baseurl }}) lists two publications under "Publications."
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In addition to the recommended publication, you should also cite the ontology using its IRI and the [new data citation extension to JATS](https://peerj.com/articles/cs-1/). When no specific publication is recommended, you must cite the ontology by its IRI. Here is an example citation:
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> Mungall, C., Haendel, M., Dahdul, W., Ibrahim, N., Segerdell, E., Blackburn, D., Comte, A., Niknejad, A., and Decechi, A. (2016), Uberon Ontology, http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl
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<div class="citation-blockquote">
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Mungall, C., Haendel, M., Dahdul, W., Ibrahim, N., Segerdell, E., Blackburn, D., Comte, A., Niknejad, A., and Decechi, A. (2016), Uberon Ontology, http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl
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</div>
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Our ontology files list authors using the [dc:creator](http://purl.org/dc/elements/1.1/creator) property. The order of authors is not important, but you can use the primary contact for the ontology listed on the [OBO site](http://obofoundry.org) as the first author. Note that this does not necessarily include all those who have contributed directly to the ontology, via its issue tracker or on its mailing lists, for example. However, these can be readily retrieved if the proper IRI is referenced in the citation.
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‎citation/KnownPublications.md‎

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---
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layout: citation
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title: Known Ontology Project Publications
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---
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This list is generated automatically from OBO Foundry ontology metadata. It is not intended to be authoritative or exhaustive.
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<div>
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{% for ontology in site.ontologies %}
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{% if ontology.publications and ontology.publications.size > 0 %}
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<h5>{{ ontology.title }} ({{ ontology.id }})</h5>
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<ul>
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{% for publication in ontology.publications %}
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<li><a href="{{ publication.id }}" target="_blank" rel="noopener">{{ publication.title }}</a></li>
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{% endfor %}
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</ul>
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{% endif %}
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{% endfor %}
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</div>

‎citation/RelatedPublications.md‎

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---
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layout: citation
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title: Publications Related to the OBO Foundry
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---
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<h2 id="citing">Citing the OBO Foundry</h2>
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To reference the OBO Foundry generally, please cite:
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Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters, **[OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies](https://academic.oup.com/database/article/doi/10.1093/database/baab069/6410158)**, Database, Volume 2021, 2021, baab069, https://doi.org/10.1093/database/baab069
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<h2 id="other">Other papers about the OBO Foundry</h2>
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Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis, **[The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](http://www.nature.com/nbt/journal/v25/n11/abs/nbt1346.html)**, Nature Biotechnology, Volume 25, 2007, https://doi.org/10.1038/nbt1346
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[Google Scholar list of papers citing The OBO Foundry](https://scholar.google.ca/scholar?cites=13806088078865650870&as_sdt=2005&sciodt=0,5&hl=en)

‎registry/publications.md‎

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