<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Joël,<div><br></div><div>Please find below answers to your first two questions:</div><div><div><div>On 17 Nov 2014, at 21:09, Joel Fillon, Mr <<a href="mailto:joel.fillon@mcgill.ca">joel.fillon@mcgill.ca</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Ensembl people,<br><br>Given a list of gene IDs from one species, I would like to retrieve the associated GO ids programmatically.<br>Species can belong to Ensembl e.g. Mus musculus or EnsemblGenomes e.g. Arabidopsis thaliana.<br><br>I managed to access them using BioMart through R although the parameters differ between Ensembl and EnsemblGenomes.<br><br>Ensembl:<br>host: <a href="http://www.ensembl.org">www.ensembl.org</a><br>mart: ENSEMBL_MART_ENSEMBL<br>dataset: <short_scientific_name>_gene_ensembl (e.g. mmusculus_gene_ensembl)<br>attributes: ensembl_gene_id, go_id<br><br>EnsemblGenomes:<br>host: <division>.<a href="http://ensembl.org">ensembl.org</a> (e.g. <a href="http://plants.ensembl.org">plants.ensembl.org</a>)<br>mart: <division>_mart_<release_number> (e.g. plants_mart_24)<br>dataset: <short_scientific_name>_eg_gene (e.g. athaliana_eg_gene)<br>attributes: ensembl_gene_id, go_accession<br><br><br>1. Are those parameters consistent across species within Ensembl and EnsemblGenomes e.g.<br>if I want ids for Bos taurus, dataset will be btaurus_gene_ensembl and attributes ensembl_gene_id, go_id<br>will be available?<br></blockquote>You are right, the parameters that you have mentioned are consistent across species within Ensembl and EnsemblGenomes.</div><div>Your example on Bos taurus will work.</div><div><blockquote type="cite"><br>Or are they likely to be modified with the DB schema in the future and I shouldn't rely on them for a systematic automated solution?<br></blockquote>We avoid changing the mart attribute internal names but if we do we will declare the changes on the following page: <a href="http://www.ensembl.org/info/website/news.html">http://www.ensembl.org/info/website/news.html</a></div><div>The mart internal names are more stable than the DB schema so you can rely on them for a systematic automated solution.<br><blockquote type="cite"><br>2. Is a go_id in Ensembl equivalent to a go_accession in EnsemblGenomes?<br></blockquote>Yes, go_id in Ensembl correspond to go_accession in EnsemblGenomes.<br><blockquote type="cite"><br>3. Is there a better way to do this using REST API or other?<br>From <a href="http://rest.ensembl.org/">http://rest.ensembl.org/</a> , I can't find an Endpoint<br>linking a gene ID to related Gene Ontologies<br><br>GET xrefs/symbol/:species/:symbol and GET xrefs/name/:species/:name seem to link to external gene databases only.<br>Also, for a list of 20000+ gene ids, I would need to use POST requests with reduced chunks I guess.<br><br>4. On a different note, sorry if this was answered before. I can't find a "Search" function on this mailing list:<br>Am I missing it on:<br><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br><br>or is search only available through Google or other with "site:http://lists.ensembl.org ..."?<br><br>Thanks a lot for your help!<br><br>Joël<br>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br>Ensembl Blog: http://www.ensembl.info/<br></blockquote></div><div><br></div>Hope this helps,</div><div>Regards,</div><div>Thomas<br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus<br>Hinxton<br>Cambridge CB10 1SD<br>United Kingdom</div></div></span></div></span></div></span></div></span>
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