NBC sign off documentation

Disease

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 nice 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.
  • caltech issue

• caltech needs to update their descriptions based on our omim data (will start asking 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 putting it as text into the accession numbers. Especially since we cover plant and animal parasites in addition.
  • Would be great

Model

• adding PODs
• see Disease.pm

Orthology

Model

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

UI

• providing development support as WB2 moves forward

Ontology

Model

• providing development support as WB2 moves forward

UI

• providing development support as WB2 moves forward

Tree_lister

• currently an external resource from dev site re-engineered to work with WB2
• location: /usr/local/wormbase/website/classic/cgi-perl/ontology/tree_lister

Search

• should be super-ceded by Xapian system

Position matrix data

Data compile

• developing module for pipeline

• Positiion matrix needs alot of work. I'll periodically jump in to fix things to try to get a compile done b/4 WS227 goes to production
• necessary code is in /home/norie/dev/position_matrix
• Steps -- roughly:

• generates instructions for R to create data files into input directory

• • create_consensus_r_files.pl
  • create_pwm_data_files.pl
  • create_pwm_r_files.pl

• take instructions from input directory and runs appropriate R processes to generate consensus files

• • generate_consensus.pl
  • generate_sl.pl
  • generate_pm_id2consensus.pl

etc...

Documentation

• ongoing