Populating dois

Current Pipeline

• Put into place in 2014-01

• Uses pmid2doi mapping service hosted by NBIC (http://www.pmid2doi.org/)

• This service has dois for many older papers for which PubMed does not have a doi

• Script that queries NBIC service is here:

/home/postgres/work/pgpopulation/pap_papers/20140107_doi_from_pmid/get_doi_from_pmid.pl

• And is called by this script here:

 /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/get_new_elegans_xml.pl

• This runs on the 19th as part of the &pubmedNotFinal routine where we query PubMed again to update metadata for papers that weren't fully indexed by PubMed when they came into WormBase (which is usually all of them).

• You can check the latest pap_identifier that are doi with Kimberly as the curator with :

 SELECT * FROM pap_identifier WHERE pap_curator = 'two1843' AND pap_identifier ~ 'doi' ORDER by pap_timestamp DESC;

• And you can probably run the script manually by logging on as acedb and pasting :

 /home/postgres/work/pgpopulation/pap_papers/20140107_doi_from_pmid/get_doi_from_pmid.pl

Pipeline Updates, 2014-07-21

Change too pap_match.pm

my @temp = ( "pmid$pmid", $doi ); # some data is %multi, so needs to be passed to &changeXmlPg as an array

Older Pipeline

Populating dois for WormBase Paper Objects

1) Add dois to papers for which we have a PubMed XML and the doi is in the XML

a) Script is on mangolassi: /home/postgres/work/pgpopulation/pap_papers/20111014_doi_pii_population/doi_pii_populate.pl

2) Add dois to newly approved papers in the paper editor

a) Update code of paper_editor.cgi and pap_match.pm - Need to confirm this

3) Add dois to papers that don't have a doi in the PubMed XML, or don't have a PubMed XML

a) Use crossref.org account b) How many papers are there? c) How do we keep track of what we've done, or should we just periodically run a query?