Difference between revisions of "NBC sign off documentation"

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* Testing
* Testing
= Orthology
= Orthology =
== Model ==
== Model ==

Revision as of 18:09, 20 July 2011


Disease search

  • Disease.ace file generated for addition to Xapian search system
  • File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data compile

Michael Paulini's development towards tighter disease incorporation

Responding to MP's notes

  • mark the elegans/worm genes with omim ortholgs, as caltech is unable to query into the proteins (done by me and will be in ws227)
    • file with the associations available from the orthology data compile -- /usr/local/wormbase/databases/{RELEASE}/orthology/go_id2omim_ids.txt
    • details of this file documented in table: [[1]]
  • put the omim descriptions into the database ... and I thought there of you and your flat files to get the data. That would end up in the accession numbers ... end they in turn would need some omim: prefix or so, as else their are just numbers
    • file with details of OMIM diseases available from the orthology data compile -- /usr/local/wormbase/databases/{RELEASE}/orthology/omim_id2disease_desc.txt
    • details of this file documented in table: [[2]]
  • would be cool if the functinality of searching through omim descriptions and showing genes connected to diseases would reappear on the new site, but I don't know how, as acedb might be a bit slowish to search through the text (but maybe it is fast enough).
    • see note re: disease search above, generated file includes requested data
  • the omim database record needs to be updated, as omim is now on www.omim.org (done by Mary Ann and will be in ws227). I don't know of it was one of our best ideas to put the urls into acedb, as it now takes two months to fix broken links, but then who cares.
    • caltech issue
  • caltech needs to move their behinds and update their descriptions based on our omim data (will start prodding them after ws227)
    • see above, info available
  • Show phenotypes of connected genes on the disease pages, as they might be handy
    • Can be done; data from the soon-to-be-deprecated CompileGeneResources has all necessary information -- /usr/local/wormbase/databases/{RELEASE}/gene
  • Kev thought of creating a disease class instead of plunking it as text into the accession numbers. Especially since we cover plant and animal parasites in addition. (Good idea, but needs some more planning)
    • Would be great


  • adding PODs
  • see Disease.pm


  • Testing



  • Information/Functionality incorporated into Gene Model; providing development support providing development support as WB2 moves forward


  • providing development support as WB2 moves forward

Paralog model additions for gene evolution

  • paralog data being ported from classic site usr/local/wormbase/website/classic/cgi-perl/orthology/gene to Gene.pm

Paralog UI for gene evolution

  • in planning stage






Position matrix data

Data compile


Miscellaneous UIs