NBC sign off documentation

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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/WS225/orthology/go_id2omim_ids.txt - details of this file documented in http://wiki.wormbase.org/index.php/Software_Life_Cycle:_1._Updating_The_Development_Server#Compiled_file_documentation_and_plans

b) 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

c) 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.

d) 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).

e) caltech needs to move their behinds and update their descriptions based on our omim data (will start prodding them after ws227)

Optional f) Show phenotypes of connected genes on the disease pages, as they might be handy

And variant B) 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)



Orthology - paralog development



Paralog model additions for gene evolution

Paralog UI for gene evolution






Position matrix data

Data compile


Miscellaneous UIs