Difference between revisions of "Populating dois"
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*Put into place in 2014-01 | *Put into place in 2014-01 | ||
| − | *Uses pmid2doi mapping service hosted by NBIC | + | *Uses pmid2doi mapping service hosted by NBIC (http://www.pmid2doi.org/) |
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| + | *This service had dois for many older papers for which PubMed does not have a doi | ||
*Script that queries NBIC service is here: | *Script that queries NBIC service is here: | ||
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*And you can probably run the script manually by logging on as acedb and pasting : | *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 | /home/postgres/work/pgpopulation/pap_papers/20140107_doi_from_pmid/get_doi_from_pmid.pl | ||
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=Older Pipeline= | =Older Pipeline= | ||
Revision as of 18:18, 30 June 2014
Current Pipeline
- Put into place in 2014-01
- Uses pmid2doi mapping service hosted by NBIC (http://www.pmid2doi.org/)
- This service had 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
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?
