View source for 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: [[http://wiki.wormbase.org/index.php/Software_Life_Cycle:_1._Updating_The_Development_Server#Compiled_file_documentation_and_plans]]

* 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: [[http://wiki.wormbase.org/index.php/Software_Life_Cycle:_1._Updating_The_Development_Server#Compiled_file_documentation_and_plans]]

* 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

= Miscellaneous UIs  =