I wrote a little AppleScript that removes some of the bogus fields that get
imported from PubMed. I think I wrote this before the switch to XML, so maybe
it needs some minor changes. It still seems to work just fine for me, though.
Paste this in Applescript editor, save as, say, CleanPubMed.scpt, and use it as
the script hook for importing references in the Preferences:
---------------------------------------------------------------------------
(*
This script will remove unofficial bibtex fields that pubmed puts in.
It should be set as a script hook for "Import Publications".
*)
property bogusFields : {"Address", "Au", "Copyright", "Crdt", "Da", "Date",
"Dcom", "Dep", "Edat", "Gr", "Issn", "Jid", "Jt", "Language", "Lr", "Mh",
"Mhda", "Oid", "Own", "Phst", "Pii", "Pl", "Pmcr", "Pst", "Pt", "Rf", "Rn",
"Sb", "So", "Stat", "Status", "Source"}
using terms from application "BibDesk"
on perform BibDesk action with publications thePubs for script hook
theScriptHook
-- get some properties from the script hook
set theName to name of theScriptHook
-- check if we get the right script hook event
if theName is not "Import Publications" then return
repeat with thePub in thePubs
-- remove period at end of title
set theTitle to title of thePub
if item -1 of theTitle = "." then
set theTitle to items 1 thru -2 of theTitle as
text
end if
tell thePub
if value of field "Pmid" is not "" then
set value of field "Title" to theTitle
-- change values of the form "2009 Jan
1" to "2009"
set theDate to get value of field "Year"
set value of field "Year" to word 1 of
theDate
-- remove bogus fields
repeat with theField in bogusFields
set value of field theField to
""
end repeat
end if
end tell
end repeat
end perform BibDesk action with publications
end using terms from
---------------------------------------------------------------------------
On Dec 20, 2009, at 8:52 AM, Christiaan Hofman wrote:
>
> On Dec 20, 2009, at 14:15, Miguel Ortiz Lombardia wrote:
>
>> Hi everyone,
>>
>> I wonder if something has changed in BibDesk 1.4 (or in PubMed, in which
>> case, of course you need not to know) with respect to the import of
>> publications found after a PubMed Search (within BibDesk). It seems that a
>> lesser number of fields is imported now. One such field that is important to
>> me is 'PST' (publication status). I used an 'intelligent group' made of
>> publications with values of PST being 'aheadofprint' or 'ppublish'. This way
>> I could go from time to time to PubMed to get these publications updated
>> once published.
>>
>
> Nothing has changed in 1.4 with PubMed import. There was a minor change 4
> months ago and we swtiched to using pubmed XML for the search group about 7
> months ago.
>
>> Is there a way to control what fields from a PubMed entry are imported?
>>
>
> No.
>
> Christiaan
>
>> Thanks in advance!
>>
>>
>>
>> -- Miguel
>>
>> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
>> CNRS, Universités d'Aix-Marseille I & II
>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>> Tel: +33(0) 491 82 55 93
>> Fax: +33(0) 491 26 67 20
>> e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
>> Web: http://www.pangea.org/mol/spip.php?rubrique2
>>
>>
>>
>>
>>
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>
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--
Mark
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