[referencer] getting metadata from pubmed and some comments

Michele Mattioni mattions at gmail.com
Tue Nov 6 19:11:07 EST 2007


+1 to really cool pubmed integration in referencer ;)

On Nov 7, 2007 12:33 AM, Leonardo Fontenelle <leo.fontenelle at gmail.com> wrote:
> I'm not (yet) a regular Referencer user, but I'm very interested in
> PubMed integration.
>
> I was following the thread and noticed the "family name, given name"
> part. I won't be able to say much about it, but I'd like to suggest
> this reading:
>
> http://rishida.net/blog/?p=100
>
> Best regards!
>
> Leonardo Fontenelle
> http://leonardof.org
>
> 2007/11/6, Aurélien Naldi <aurelien.naldi at gmail.com>:
>
> > Hi,
> >
> > I'm a computer scientist by formation now working in bioinformatics.
> > As such I am dealing with tons of biology papers. I have found
> > referencer to be a great tool, the metadata fetching through crossref
> > is nice, but I never got more than the familly name of the first
> > author in the author field. Pubmed has much more complete metadata for
> > the papers I am currently dealing with, I would thus like to know if
> > adding support for pubmed into referencer is possible.
> >
> > I have just looked at how to get metadata through pubmed, here is a
> > quick introduction:
> >
> > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=20&retstart=0&term=<!your_search_term!>
> >
> > pointing to this will give you a list of matches under this form:
> >
> >
> > <eSearchResult>
> >         <Count>1</Count>
> >         <RetMax>1</RetMax>
> >         <RetStart>0</RetStart>
> >         <IdList>
> >                 <Id>17581588</Id>
> >         </IdList>
> >         <TranslationSet>
> >         </TranslationSet>
> >         <TranslationStack>
> >                 <TermSet>
> >                         <Term>10.1038/nature05970[All Fields]</Term>
> >                         <Field>All Fields</Field>
> >                         <Count>1</Count>
> >                         <Explode>Y</Explode>
> >                 </TermSet>
> >                 <OP>GROUP</OP>
> >         </TranslationStack>
> >         <QueryTranslation>10.1038/nature05970[All Fields]</QueryTranslation>
> > </eSearchResult>
> >
> >
> > The important part is the IdList, it gives the list of PMID matching
> > with the search. To get more data on a particular entry, use this URL:
> >
> > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=citation&id=<!PMID!>
> >
> > The result is a huge XML file with a real list of author, abstract,
> > and much more.
> > Some documentation (which I have not really read yet) is available at
> > http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=coursework.section.brief
> >
> > I have not seen an explicit search by doi but searching a doi does
> > work (without the "doi:" prefix)
> >
> > AFAIK, PDFs unfortunatly don't include a PMID, but this gives much
> > better results than crossref for biology papers...
> >
> > While I am at it, I have some (naive) questions about your XML format:
> > * Is it referencer-specific ?
> > * What are its advantages over bibtex XML (or other similar stuff) ?
> > It seems to deal better with "tags" (bibtexxml has keywords) and
> > pdffilenames (bibtexxml  has only a relative path, when exported with
> > jabref) and to add the "manage_target" thing, that I do not use (yet).
> > Is it anything else ?
> > * I see only one "authors" field, which is way too "bibtex like" for
> > my taste. Having a clean separation of authors and being able to split
> > family name and given name looks nice to me.
> > Is it possible to extend the format to deal with this ?
> >
> > And a final coment: some of my pdf files did not contain a doi entry,
> > when adding a whole directory, I got one error dialog for each of
> > them. It would be much more useful to remember the list of problematic
> > files and to show the list at the end of the process. Giving them a
> > "this thing need work" tag could be nice also, what do you think about
> > this ?
> >
> > Thanks for your work on this nice tool!
> >
> > Best regards.
> >
> > --
> > Aurélien Naldi
> >
>


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