Difference between revisions of "Getting Papers into WormBase"

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*This is how I've been uploading papers as of ~February 2009:
 
*This is how I've been uploading papers as of ~February 2009:
**Every day at 6AM PST, an automated script accesses [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] to perform a search using the keyword elegans.
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**Every day at 6AM PST, an automated script accesses [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] to perform a search using the keyword 'elegans'.
 
**The results of this search are presented in the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi wbpaper_editor.cgi].   
 
**The results of this search are presented in the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi 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!'
 
**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!'

Revision as of 15:08, 20 May 2009

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: