<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nathalie,<div><br></div><div>we have phenotype data from EuroPhenome and MGP. You can find more about the sources here: <a href="http://www.ensembl.org/info/genome/variation/sources_documentation.html#mus_musculus">http://www.ensembl.org/info/genome/variation/sources_documentation.html#mus_musculus</a></div><div><br></div><div>We have only gene associated phenotypes for mouse.</div><div><br></div><div>Thanks,</div><div>Anja<br><div><div>On 24 Jul 2014, at 15:40, Nathalie Conte wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Anja, I have successfully retrieved phenotypes with fetch_all_by _gene method.<br>I am retrieving so far data from MGP with KO gene - is there any other data sources for mouse phenotypes, what about variation phenotypes ?<br><br>script<br>my $pfs = $pf_adaptor->fetch_all_by_Gene($gene);<br>if ( scalar(@$pfs)== 0 ){print "no PHE\n";}else{<br>foreach my $pm(@{$pfs}){ if ($pm){<br>print "\t", $pm->allele_symbol,"\t",$pm->source,"\t",$pm->phenotype->description, "\n";<br>}else {next;} <br><br>Thanks<br>N<br><br>On 23 Jul 2014, at 16:52, Anja Thormann <<a href="mailto:anja@ebi.ac.uk">anja@ebi.ac.uk</a>> wrote:<br><br><blockquote type="cite">Hello Nathalie,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">we have only genes associated with phenotypes for mouse. You need to use fetch_all_by_Gene.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Kind regards,<br></blockquote><blockquote type="cite">Anja<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 23 Jul 2014, at 16:46, Nathalie Conte wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi , <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is there mouse phenotypes available through the ensembl API ?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am trying to retrieve mouse phenotypes from the API using the phenotype feature adaptor = Bio::EnsEMBL::Registry->get_adaptor('mouse', 'variation', 'phenotypefeature'),<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">using fetch_all_by_Variation method, and cannot retrieve any -<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please advise,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Nathalie<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br></blockquote><blockquote type="cite">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></body></html>