faq.html

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title: FAQ
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	  Frequently Asked Questions (FAQ)
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	<h3>How do I join the OBO Foundry?</h3>
	<p>
	  Joining is easy! Just follow the steps on our
	  <a href="join.shtml"><b>join</b></a> page. We look forward to hearing
	  from you.
	</p>
	
	<h3>How should I cite the OBO Foundry?</h3>
<p>
Smith B, Ashburner M, Rosse C, Bard C,
      Bug W, Ceusters W, Goldberg L J, Eilbeck K,
      Ireland A, Mungall C J, The OBI Consortium,
      Leontis N, Rocca-Serra P, Ruttenberg A,
      Sansone S-A, Scheuermann R H, Shah N,
      Whetzel P L and Lewis S (2007).
<a href="http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html">
"The OBO Foundry: coordinated evolution of ontologies to support
      biomedical data integration",
<i>Nature Biotechnology</i> 25, 1251 - 1255.</a>

<h3>Are the ontologies in the OBO Foundry available only in OBO format?</h3>
<p>
No!  
<a href="http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page">Here is a definition of the OBO language in terms of
OWL semantics</a>.
You can download any OBO ontology in various formats--including OWL--<a href="http://www.berkeleybop.org/ontologies">here</a>.
</p>

<h3>Is there a tool that will let me create or edit OBO
ontologies?</h3>

<p><a href="http://www.oboedit.org/">OBO-Edit</a>, an open source Java
tool, offers a convenient visual interface for creating, editing, and browsing ontologies.
It was initially created to work on OBO-format ontologies, but is currently
being extended to handle other ontology formats, such as OWL.
</p>

	<h3>How should we resolve conflicts when ontologies overlap?</h3>
	<p>
	  Make every attempt to resolve inconsistencies and merge the
	  ontologies. Tools are available for aiding this process
	  (such as <a href="https://web.archive.org/web/20090924102802/http://www.berkeleybop.org:80/obol/">OBOL</a>
	  and <a
	  href="http://protege.cim3.net/cgi-bin/wiki.pl?Prompt">Prompt</a>)
	  and the community can be used to help clarify best
	  practices.

	  Also, face-to-face meetings can helpful to resolve details
	  that cannot be covered through email.
	</p>
	
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