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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Hi Bruce,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">the
<span class="SpellE">genbank</span> is done via <span class="SpellE">ncbi</span> <span class="SpellE">
entrez</span>.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">With “<span class="SpellE">showserver</span>” you can see where the configuration file is located (default is /<span class="SpellE">usr</span>/local/emboss/share/EMBOSS/<span class="SpellE">server.entrez</span>).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">In this file you can see, which
<span class="SpellE">ncbi</span> databases are configured and which fields can be queried.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">So to get a
<span class="SpellE">refseq</span> <span style="mso-spacerun:yes"> </span>you can use:<span style="mso-spacerun:yes">
</span>“<span class="SpellE">entret</span> <span class="SpellE">entrez:nucleotide:NM</span>_.....”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">But for unknown reasons on my system it takes in the range of a minute before the entry is returned. This issue can be
related to our firewall.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Therefore I use for
<span class="SpellE">ncbi</span> an alternative solution:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">I have configured this database definition:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-ansi-language:DE">--------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-ansi-language:DE">DB
<span class="SpellE">ncbin</span> [<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-ansi-language:DE"><span style="mso-spacerun:yes">
</span>type: N<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-ansi-language:DE"><span style="mso-spacerun:yes">
</span><span class="SpellE">format</span>: <span class="SpellE">genbank</span><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-ansi-language:DE"><span style="mso-spacerun:yes">
</span></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">method: app<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><span style="mso-spacerun:yes">
</span>app: "/<span class="SpellE">usr</span>/local/emboss/bin/<span class="SpellE">ncbi_fetch</span> nucleotide:%s"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><span style="mso-spacerun:yes">
</span>comment: "NCBI <span class="SpellE">GenBank</span> Nucleotide" ]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">---------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span class="SpellE"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">ncbi_fetch</span></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">
is<span style="mso-spacerun:yes"> </span>a simple <span class="SpellE">perl</span> script using
<span class="SpellE">wget</span> to call the <span class="SpellE">ncbi</span> <span class="SpellE">
eutils</span>.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">-------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">#!/<span class="SpellE">usr</span>/local/bin/<span class="SpellE">perl</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"># %s passed from emboss
<span class="SpellE">entret</span> or <span class="SpellE">seqret</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">$id=$ARGV[0];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">$entry=`/<span class="SpellE">usr</span>/local/bin/<span class="SpellE">wget</span> --wait=3 --<span class="SpellE">waitretry</span>=3
-q --cache=off --timeout=10 -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$id&rettype=gb&retformat=text"`;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">print $entry;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">--------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Hope this helps.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">David.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:DE">Von:</span></b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:DE">
emboss-bounces+david.bauer=bayer.com@mailman.open-bio.org [mailto:emboss-bounces+david.bauer=bayer.com@mailman.open-bio.org]
<b>Im Auftrag von </b>Citron, Bruce A.<br>
<b>Gesendet:</b> 04 December 2014 20:07<br>
<b>An:</b> EMBOSS@mailman.open-bio.org<br>
<b>Betreff:</b> [EMBOSS] Remote Databases and possibly drcat<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue">What do I need to do, or have our IT guy adjust, to be able to grab sequences from ncbi (genbank, refseq, etc.) into
my directory on a LINUX mainframe? This used to work under GCG via net fetch. I'm using <span class="apple-style-span">EMBOSS 6.6.0.0, command line.</span></span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue">I can use seqret to grab embl sequences (seqret embl:accession) and that works fine, however none of the synonyms that
I can think of for genbank work.</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue">Should our system have access through drcat? I do see Genbank, and many other remotes listed there. I'm not sure how
that works.</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue">I'm also not sure why it accesses embl sequences because embl isn't listed by showdb.</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue">showdb produces:</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">Display information on configured databases</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue"># Name Type Comment</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue"># ============= ======== =======</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">taxon Taxonomy NCBI taxonomy</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">drcat Resource Data Resource Catalogue</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">chebi Obo Chemical Entities of Biological Interest</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">eco Obo Evidence code ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam Obo EMBRACE Data and Methods ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam_data Obo EMBRACE Data and Methods ontology (data)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam_format Obo EMBRACE Data and Methods ontology (formats)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam_identifier Obo EMBRACE Data and Methods ontology (identifiers)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam_operation Obo EMBRACE Data and Methods ontology (operations)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">edam_topic Obo EMBRACE Data and Methods ontology (topics)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">go Obo Gene Ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">go_component Obo Gene Ontology (cellular components)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">go_function Obo Gene Ontology (molecular functions)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">go_process Obo Gene Ontology (biological processes)</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">pw Obo Pathways ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">ro Obo Relations ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">so Obo Sequence ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Courier;mso-fareast-font-family:"Times New Roman";color:blue">swo Obo Software ontology</span><span style="font-size:10.5pt;mso-fareast-font-family:"Times New Roman";color:blue"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue"><o:p> </o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white"># Name Type Comment</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white"># ============= ======== =======</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">taxon Taxonomy NCBI taxonomy</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">drcat Resource Data Resource Catalogue</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">chebi Obo Chemical Entities of Biological Interest</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">eco Obo Evidence code ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam Obo EMBRACE Data and Methods ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam_data Obo EMBRACE Data and Methods ontology (data)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam_format Obo EMBRACE Data and Methods ontology (formats)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam_identifier Obo EMBRACE Data and Methods ontology (identifiers)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam_operation Obo EMBRACE Data and Methods ontology (operations)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">edam_topic Obo EMBRACE Data and Methods ontology (topics)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">go Obo Gene Ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">go_component Obo Gene Ontology (cellular components)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">go_function Obo Gene Ontology (molecular functions)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">go_process Obo Gene Ontology (biological processes)</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">pw Obo Pathways ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">ro Obo Relations ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">so Obo Sequence ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:white">swo Obo Software ontology</span><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";color:blue"><o:p> </o:p></span></p>
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