Getting Papers into WormBase

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From Kimberly:

  • This is how I've been uploading papers as of ~February 2009:
    • Every day at 6AM PST, an automated script accesses PubMed to perform a search using the keyword elegans.
    • The results of this search are presented in the wbpaper_editor.cgi.
    • To enter new papers, select your name from the curator list, scroll down to the bottom of the page, and click on the link that says, 'Enter New Papers!'
    • The New Papers page lists the PMID and abstract for each of the returned papers. Alongside each of the abstracts is a radio button where a curator can elect to accept or reject the paper.
    • Papers that are accepted will be subsequently processed and receive a WBPaper ID.
    • The PMIDs for rejected papers are stored in a file (/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids) to be used as a negative training set for machine learning approaches to paper identification (triage).
  • Papers that I accept: