automatic bibtex (was Re: [Skim-app-users] Updating references)

[Thomas Schneider]

Jason:

> For a lot of the manuscript and grant applications I have to include
> the pmid and PMC numbers that pubmed provides. I've added the Pmc
> filed as a default for all references. This works just fine for new
> references, but is blank in my previous references. I really don't
> want to go through the processes of re-importing, dealing with
> duplicates etc. because that would take a long time. How can I
> simply update my references?

Since this is not related to Skim display, this discussion would be
better held on the texhax news group (texhax at tug.org
https://tug.org/mailman/listinfo/texhax) so I am ccing there and
suggest that after this we remove the Skim references.

I have a tcsh script (!) that calls a Pascal (!) program:

https://alum.mit.edu/www/toms/ftp/medquery
https://alum.mit.edu/www/toms/delila/medlinebib.html

Given a PubMed Id (pmid) together they grab the reference format and
create a Bibtex entry.  Then they look in my bibliography file to see
if the same key has been used before (first author, last author, year
which is nearly unique in PubMed).  If so, they are compared using
sdiff.  If the new entry has a doi, that is provided in a file.  I
then edit my bibliography file BY HAND to upgrade the reference.  I do
it by hand to avoid disasters of programs doing unexpected things.

Tom

  Thomas D. Schneider, Ph.D.
  Senior Investigator
  National Institutes of Health
  National Cancer Institute
  Center for Cancer Research
  RNA Biology Laboratory
  Biological Information Theory Group
  Frederick, Maryland  21702-1201
  schneidt at mail.nih.gov
  https://alum.mit.edu/www/toms