[Go] Reporting invalid PubMed IDs - central location?

[Jim Hu]

It might actually be possible to build this into the validation  
scripts, but if it's really rare, that may not be worth it.

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.

Jim

On Jun 15, 2009, at 11:51 AM, vanauken at caltech.edu wrote:

> Dear Donna,
>
> Thank you for writing to the GO and raising the issue about reporting
> invalid PubMed IDs.
>
> I have cc'ed the general GO mailing list on this email to see if it  
> would
> be possible to set up a central place to report invalid PMIDs, or if
> someone might perhaps have another suggestion for how to communicate  
> this
> information to the various MODs efficiently.
>
> Best,
> --Kimberly Van Auken
>
> Database Curator, WormBase
> www.wormbase.org
> www.geneontology.org
>
>
>
>> Subject: validating PubMed ids in the gene association files
>> Date: Mon, 15 Jun 2009 12:18:49 -0400
>>
>> Hello all,
>> In our processing of gene_association files on the ftp site for  
>> Entrez
>> Gene, we periodically (and rarely) find PubMed uids that are not  
>> valid.
>>
>> Is there a central location to which we can report these invalid  
>> PubMed
>> uids that can be checked by each data source?
>>
>> We are hoping for one reporting site, rather than gmod-specific ones.
>>
>> Thanks for your help,
>>
>> Donna Maglott                             maglott at ncbi.nlm.nih.gov
>> ------------------------------------------------------------------------------
>>   National Center for Biotechnology Information
>>  National Library of Medicine, NIH                phone:    
>> 301-435-5895
>>   Building 45, Room 4As.47C
>> fax:    301-480-0109
>>   Bethesda, MD 20892-6510
>> ------------------------------------------------------------------------------
>>
>>
>>
>>
>
>
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> Go at geneontology.org
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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