Understand the pipeline by looking at all scripts and forms
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List of scripts and forms to talk about
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 /home/postgres/work/pgpopulation/pap_papers/new_papers/pap_match.pm
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 (?) /home/postgres/work/pgpopulation/afp_papers/assign_passwd.pl
I'm sure there are more scripts and forms like :
(???) 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.