Difference between revisions of "NBC sign off documentation"

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= Disease =
 
= Disease =
== disease search ==  
+
== Disease search ==  
 
*Disease.ace file generated for addition to Xapian search system
 
*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
 
* File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data compile
  
 
==  Michael Paulini's development towards tighter disease incorporation ==
 
==  Michael Paulini's development towards tighter disease incorporation ==
== Model ==
 
== UI/test ==
 
  
 +
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 =
  
= orthology - paralog development =
+
== Model ==
== Model ==
+
* Information/Functionality incorporated into Gene Model; providing development support providing development support as WB2 moves forward
 
== UI ==
 
== UI ==
== paralog model additions for gene evolution ==
+
* providing development support as WB2 moves forward
== paralog UI for gene evolution ==
+
= Ontology =  
 
 
= ontology =  
 
 
== Model ==  
 
== Model ==  
 +
* providing development support as WB2 moves forward
 
== UI ==  
 
== UI ==  
== tree_lister ==  
+
* providing development support as WB2 moves forward
== search ==  
+
== 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...
  
= position matrix data =  
+
== Documentation ==
o data compile
+
* ongoing
o documentation
 
  
= miscellaneous UIs  =  
+
= Miscellaneous UIs  =
o
 

Latest revision as of 20:22, 29 July 2011

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

Miscellaneous UIs