[openbiblio-dev] Medline and UKPMC bibliography

Thu Feb 2 18:05:25 UTC 2012

On Thu, Feb 2, 2012 at 3:07 PM, Tom Morris <tfmorris at gmail.com> wrote:

> n Thu, Feb 2, 2012 at 4:07 AM, Peter Murray-Rust <pm286 at cam.ac.uk> wrote:
> > I am compiling a small bibliography by searching for "snowy owl" in UKPMC
> > and Pubmed. I haven't yet found how to export bibliography from UKPMC.
> The
> > Medline bibliography looks like:
> >
> > PMID- 19894598
> > OWN - NLM
> > STAT- MEDLINE
> > DA  - 20091109
> > DCOM- 20100319
> > IS  - 1026-3470 (Print)
> > IS  - 1026-3470 (Linking)
> > IP  - 5
> > DP  - 2009 Sep-Oct
> > TI  - [Red-breasted goose colonies on the Taimyr Peninsula: factors
> > responsible for the
> >       proximity of goose nests to nests of peregrine falcons,
> rough-legged
> > buzzards,
> >       and snowy owls].
> > PG  - 559-68
> >
> > This looks like RIS or an extended RIS. I think it will be valuable to
> > support it if we are going to use it as a central resource.
>
> This 2007 thread discussing how to import MEDLINE format into Zotero
> might help provide some suggestions on techniques and pointers to
> tools: http://forums.zotero.org/discussion/466/medline-format/
>
> Tom
>

Thanks,
Looks like Pubmed have taken the basic RIS format and added their own
stuff. We have two options:

* build a general RIS parser that takes stuff like this, and perhaps
creates local namespaced items based on heuritics
* build a specific Medline parser by copying and hacking the current one.

The major challenges
* knowing the complete medline vocabulary (in this area the more you parse
the more tags emerge)
* knowing what to translate each tag into.

It's a really good opportunity for someone to learn some simple python, and
to make an important contribution

P.

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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