https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422010-05-24T13:37:38ZArvadosGET-Evidence - Bug #506: Standardize gene names (correctly)https://dev.arvados.org/issues/506?journal_id=21192010-05-24T13:37:38ZTom Cleggtom@curii.com
<ul></ul><p>The "incorrect fix" has been backed out, although there are still (probably) cases of multiple variants that refer to the same gene under different names.</p> GET-Evidence - Bug #506: Standardize gene names (correctly)https://dev.arvados.org/issues/506?journal_id=21202010-06-08T11:52:05ZMadeleine Ballmpball@gmail.com
<ul></ul><p>BLM and RECQL3 both refer to the same gene (UCSC currently uses BLM rather than RECQL3). In GET we have 2 OMIM imported variants in RECQL3 but all genomes are processed as BLM.</p> GET-Evidence - Bug #506: Standardize gene names (correctly)https://dev.arvados.org/issues/506?journal_id=21702011-02-15T15:17:31ZWard Vandewegeward@curii.com
<ul><li><strong>Project</strong> changed from <i>19</i> to <i>GET-Evidence</i></li><li><strong>Category</strong> deleted (<del><i>GET-Evidence</i></del>)</li></ul> GET-Evidence - Bug #506: Standardize gene names (correctly)https://dev.arvados.org/issues/506?journal_id=21932011-02-16T14:44:39ZMadeleine Ballmpball@gmail.com
<ul></ul><p>Changes in the transcript file we use means that gene names now produced are almost forced to be a name that is in HGNC gene names and consistent with chromosome info (if available):</p>
<p>HGNC list:<br /><a class="external" href="http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=onlevel=pri&=on&order_by=gd_app_sym_sort&limit=&format=text&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag&&where=&status=Approved&status_opt=1&submit=submit&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_refseq_ids">http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=onlevel=pri&=on&order_by=gd_app_sym_sort&limit=&format=text&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag&&where=&status=Approved&status_opt=1&submit=submit&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_refseq_ids</a></p>
<p>Names are added by <a class="source" href="https://dev.arvados.org/projects/get-evidence/repository/8/entry/server/script/getCanonicalWithName.pl">source:server/script/getCanonicalWithName.pl</a><br />(It's still possible to have a non-HGNC name, but only if you couldn't find an HGNC name after trying all the steps outlined in the above script.)</p>
<p>I think we should consider removing all GET-Evidence entries that are not in one of the imported databases (OMIM/PharmGKB/etc) and were only found in one of the old genome processing runs -- this will clean out messed up placements and gene names that will never be looked at again. There may still be some nonstandard gene names from OMIM but I think that's less of a concern.</p> GET-Evidence - Bug #506: Standardize gene names (correctly)https://dev.arvados.org/issues/506?journal_id=21942011-02-16T14:45:03ZMadeleine Ballmpball@gmail.com
<ul><li><strong>Priority</strong> changed from <i>High</i> to <i>Normal</i></li></ul>