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<p>The simplest way I know of to obtain these mappings is to download one of the ID mapping files provided on the Uniprot web site and documented here:</p>
<p><a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/README" title="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/README
Ctrl+Click or tap to follow the link">ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/README</a><br>
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<p>In particular, the <span style="white-space: pre-wrap; font-size: 12pt;">idmapping_selected.tab file for your species of interest gives mappings to Ensembl Gene, Transcript, and Protein identifiers.</span></p>
<p><span style="white-space: pre-wrap; font-size: 12pt;"><br>
</span></p>
<p><span style="white-space: pre-wrap; font-size: 12pt;">Uniprot and Swissprot identifiers are among the available choices for External ID in Biomart on the Ensembl side, but I have found the Uniprot mappings file very convenient because it gives a large number
of other identifiers that I frequently encounter.</span></p>
<p><span style="white-space: pre-wrap; font-size: 12pt;"><br>
</span></p>
<p><span style="white-space: pre-wrap; font-size: 12pt;">Another extremely useful download, if you are working with human genes, is at HGNC:</span></p>
<p><span style="white-space: pre-wrap;"><a href="http://www.genenames.org/help/download" id="LPlnk641010">http://www.genenames.org/help/download</a></span><br>
This gives Ensembl and Uniprot identifiers, as does the Uniprot download. The HGNC download also has some extremely useful content that is
<b>not readily available elsewhere</b>, such as previously-approved HGNC symbols and
<b>synonyms</b>. I have found the synonyms and previous symbols fields from HGNC of great value for mapping lists of identifiers from sources that failed to use current approved symbols with consistency. However, I also find that mappings based on synonyms
require human checking before they can be trusted, because more than one gene may have the same synonym.</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> dev-bounces@ensembl.org <dev-bounces@ensembl.org> on behalf of Marc P. Hoeppner <mphoeppner@gmail.com><br>
<b>Sent:</b> Tuesday, June 23, 2015 6:42 AM<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> [ensembl-dev] Question about Supporting evidence / Core API</font>
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<div>Dear EnsEMBL team,<br>
<br>
Using EnsEMBL 79, I am trying to generate a best-guess mapping between Uniprot accession numbers and EnsEMBL transcripts. First, I tried:<br>
<br>
fetch_all_by_external_name ()<br>
<br>
But I noticed that this was leaving a lot of Uniprot accessions unmapped. I then checked on the website and found that these Uniprot accession tend to come up as "Supporting evidence". However, trying
<br>
<br>
my $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence($accession,"protein_align_feature");<br>
<br>
didn't seem to work. I am probably missing something about how this data is connected internally - are there feature sources other than "protein_align_feature" and "dna_align_feature", or does this connect via another adapter?<br>
<br>
An example where this is not working for me would be Uniprot entry A0M8Q6 <br>
<br>
Kind regards,<br>
<br>
Marc<br>
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