[Bioperl-l] PubMed records (was: MeSH terms)

[Chris Fields]

On Oct 25, 2009, at 6:12 AM, Peter wrote:

> On Sat, Oct 24, 2009 at 6:45 PM, Robert Bradbury
> <robert.bradbury at gmail.com> wrote:
>>  <alsaplayer-devel at lists.tartarus.org>
>> I'm not sure if this is related to the MeSH question question or  
>> not, but
>> I've googled the documentation several times and never managed to  
>> find
>> "robust" examples for how to manipulate PubMed records.
>>
>> It would seem that there ought to be code lying around which does:
>>  Given Genbank ID,
>>     Fetch all Pubmed records from that ID
>>         Fetch all related records (via NCBI's "related" record IDs)
>
> Isn't this exactly what the NCBI's ELink is for?
>
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html
>
> You'd need to work out which of the Entrez databases you are
> starting from (probably protein or genome), and then the relevant
> ELink command (maybe genome_pubmed, or protein_pubmed,
> protein_pubmed or protein_pubmed_weighted look possible).
> Then for related pubmed articles, the ELink command is just
> pubmed_pubmed.
>
> Peter

Agreed.  This should be possible through BioPerl's  
Bio::DB::EUtilities.  I'll try to post an example up.

chris