Understand the pipeline by looking at all scripts and forms

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List of scripts and forms to talk about

Paper Tables

Paper Editor


URL: http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi

    Associated scripts:  script that checks PubMed daily for new papers
                         script that checks PubMed monthly for completing bibliographic data (i.e., to make PubMed final)
    Editor functions: approve, reject, remove papers
                      create paper objects for approved papers
                      add and edit paper-associated data
    Adding and Editing Paper-Associated Data
         Genes: added via script from abstract when paper is approved
                     see Attaching Genes to Papers for more details on this and proposed changes
                added manually via a curator
                added via script from the first-pass form with evidence 'curator first pass cfp_genesymbol'
  The perl module to create papers from pubmed IDs or abstracts


 Get .ace file for Michael (how does the citace upload work

differently ?) /home/postgres/public_html/michael/get_all_papers.pl

 I don't know what this does, something about concise description and

invalid papers : /home/postgres/work/pgpopulation/wpa_papers/update_wbpaper_merging/postgres_fixing/find_merged_entries.pl

 gets merged papers from :


 (we should probably look at that CGI)
 Not sure, probably get list of new pubmed entries for form

verification and sorting : /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/get_new_elegans_xml.pl

I don't know if first pass / author first pass is part of what we need to discuss.





 to get emails from textpresso for author first pass
 mails authors for first pass (?)

I'm sure there are more scripts and forms like :

(looking at site map) http://tazendra.caltech.edu/~postgres/cgi-bin/wpa_xref.cgi http://tazendra.caltech.edu/~postgres/cgi-bin/wpa_xref_backwards.cgi

(???) genefunction.cgi Checkout papers to curate gene_function only. http://tazendra.caltech.edu/~postgres/cgi-bin/genefunction.cgi

confirm_paper.cgi Verify grouped Authors and Persons. http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/confirm_paper.cgi

generic.cgi Generic public tasks. (show ip, verify papers, update obo_ for app_tempname) http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi

paper_display.cgi display pap tables's paper data http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_display.cgi

paper_obo.cgi display WBPaper's obo http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi

pmid_wo_pdf.cgi Table of WBPapers with PMID without a PDF http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/pmid_wo_pdf.cgi

paper.cgi Group Person data with Paper with help form Author http://tazendra.caltech.edu/~postgres/cgi-bin/cecilia/paper.cgi

but the Genetics pipeline isn't in that list. And there's nothing about scripts for organizing or downloading PDFs. And I'm sure there's other people that have some paper-related forms and scripts.

We need to find out what all of them are so that it can be documented and proposed changes can make sense.

I think once we have a list we can decide where to start going through it.