<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 Magali,<div><br><div>Thanks so much for your helpful reply, that is really useful to know.</div><div><br></div><div>Thank you!</div><div><br></div><div>Regards,</div><div>Avril</div><div><br><div><div>On 13 Mar 2014, at 17:17, mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hi Avril,<br>
<br>
The system we are using is very similar to what you are describing.<br>
<br>
The main differences I can think of are:<br>
<br>
- we only project HGNC, MGI and ZFIN_ID gene names, not Uniprot or
RefSeq<br>
<br>
- we only project between one-to-one orthologs for most species<br>
for fish species, we project between one-to-many orthologs<br>
<br>
- for ontologies, we keep the same and do not look for the ancestor<br>
we do, however, filter based on species (mammal-specific go terms
should not be projected onto birds for example)<br>
For this, there is a taxon-based constraint filter provided by GO:<br>
<a class="moz-txt-link-freetext" href="http://www.ebi.ac.uk/QuickGO/GValidate?service=taxon&action=getConstraints">http://www.ebi.ac.uk/QuickGO/GValidate?service=taxon&action=getConstraints</a><br>
<br>
We also try whenever possible to project only between relatively
close species, so are not including worm, fruitfly or seasquirt in
the projections.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 13/03/2014 09:17, alc wrote:<br>
</div>
<blockquote cite="mid:845e72172bbf8e86200d8b70d54ddbcf@sanger.ac.uk" type="cite"><p>Dear Ensembl developers and users,</p><p>I'm involved in some helminth genome sequencing projects in my
group, and my colleague (Eleanor Stanley) has built an-house
Compara database for these genomes, from which we have inferred
orthologs.</p><p>I'm planning to to project protein names and GO terms across
species. I know that the Ensembl team do this already, but can't
find many details of how it's done on the web.</p><p>I'm wondering whether my plan is very different from the
Ensembl one, here is what I'm thinking of doing:</p><p>(i) Projecting protein names: for each gene in a query species
(eg. Strongyloides ratti), identify its one-to-one and
many-S.ratti-to-one orthologs in C. elegans, S. mansoni, human,
D. melanogaster, zebrafish in our local Compara database. Take a
protein name from a curated UniProt entry for one of these
orthologs (taking orthologs from those species in order of
preference given above), and project it to the query gene. Give
the projected protein name evidence code ECO:0000265 and give
the UniProt accession of the source protein. If the same protein
name is projected to several query genes, then number then with
Arabic numerals, as described in the UniProt protein naming
guide <a class="moz-txt-link-abbreviated" href="http://www.uniprot.org/docs/nameprot">www.uniprot.org/docs/nameprot</a> I couldn't find much
information on the web about how Ensembl project protein names
so am wondering is this very different?</p><p>(ii) Projecting GO terms: for each gene in a query species (eg.
Strongyloides ratti), identify all its orthologs (one-to-one,
one-to-many, many-to-one, many-to-many) in C. elegans, S.
mansoni, human, D. melanogaster, zebrafish in our local Compara
database. Take manually curated GO terms of types
IDA/IEP/IGI/IMP/IPI (excluding 'protein binding') from the
orthologs. For each pair of ortholog genes from two different
species, find the last common ancestors of their GO terms in the
GO hierarchy: project these ancestral GO terms to the query
gene. Do this for each pair of ortholog genes from two different
species. Give the projected GO terms evidence code 'IEA' and
give the UniProt accessions of the source proteins. [Note: by
transferring the last common ancestors of GO terms from
orthologs from two different species, I hope to be conservative
and just project GO terms that are likely to be conserved across
species.] I found some information on how Ensembl project GO
terms on the web (<a moz-do-not-send="true" href="http://www.ebi.ac.uk/GOA/compara_go_annotations">http://www.ebi.ac.uk/GOA/</a><a moz-do-not-send="true" href="http://www.ebi.ac.uk/GOA/compara_go_annotations">compara_go_annotations</a>),
but am not sure if the GO hierarchy is used at all as in my
idea, or if all GO terms are directly projected from orthologs
to the query gene?</p><p>Is this very different to what the Ensembl team are doing? I
would be very grateful to hear of any differences.</p><p>Kind Regards,</p><p>Avril</p><p>Avril Coghlan</p><p>Parasite Genomics Team</p><p>Sanger Institute </p>
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