<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">It might actually be possible to build this into the validation scripts, but if it's really rare, that may not be worth it. <div><br></div><div>E-Utils will accept single queries with large numbers of PMIDs, and the PMIDs in a gaf could be checked locally against the xml return. After doing this the first time, one could make the script only check new annotations, so the query wouldn't even have to be ridiculously huge.<div><br></div><div>Jim</div><div><br><div><div>On Jun 15, 2009, at 11:51 AM, <a href="mailto:vanauken@caltech.edu">vanauken@caltech.edu</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Donna,<br><br>Thank you for writing to the GO and raising the issue about reporting<br>invalid PubMed IDs.<br><br>I have cc'ed the general GO mailing list on this email to see if it would<br>be possible to set up a central place to report invalid PMIDs, or if<br>someone might perhaps have another suggestion for how to communicate this<br>information to the various MODs efficiently.<br><br>Best,<br>--Kimberly Van Auken<br><br>Database Curator, WormBase<br><a href="http://www.wormbase.org">www.wormbase.org</a><br>www.geneontology.org<br><br><br><br><blockquote type="cite">Subject: validating PubMed ids in the gene association files<br></blockquote><blockquote type="cite">Date: Mon, 15 Jun 2009 12:18:49 -0400<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hello all,<br></blockquote><blockquote type="cite">In our processing of gene_association files on the ftp site for Entrez<br></blockquote><blockquote type="cite">Gene, we periodically (and rarely) find PubMed uids that are not valid.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is there a central location to which we can report these invalid PubMed<br></blockquote><blockquote type="cite">uids that can be checked by each data source?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">We are hoping for one reporting site, rather than gmod-specific ones.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks for your help,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Donna Maglott maglott@ncbi.nlm.nih.gov<br></blockquote><blockquote type="cite">------------------------------------------------------------------------------<br></blockquote><blockquote type="cite"> National Center for Biotechnology Information <br></blockquote><blockquote type="cite"> National Library of Medicine, NIH phone: 301-435-5895<br></blockquote><blockquote type="cite"> Building 45, Room 4As.47C <br></blockquote><blockquote type="cite">fax: 301-480-0109<br></blockquote><blockquote type="cite"> Bethesda, MD 20892-6510<br></blockquote><blockquote type="cite">------------------------------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br><br>_______________________________________________<br>Go mailing list<br>Go@geneontology.org<br>http://fafner.stanford.edu/mailman/listinfo/go<br></div></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">=====================================</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Jim Hu</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Associate Professor</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Dept. of Biochemistry and Biophysics</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">2128 TAMU</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Texas A&M Univ.</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">College Station, TX 77843-2128</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">979-862-4054</font></p></div><br class="Apple-interchange-newline"></span> </div><br></div></div></body></html>