[openbiblio-dev] Medline and UKPMC bibliography

[Mark MacGillivray]

We already have a basic ris parser, and it would accept any unknown short
codes as keys anyway. If there are custom ones that people want to see
added, they could be. Or our parser could beer taken and extended and run
elsewhere.
On Feb 2, 2012 6:05 PM, "Peter Murray-Rust" <pm286 at cam.ac.uk> wrote:

>
>
> 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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>
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