Difference between revisions of "NBC sign off documentation"

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* 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)
 
* 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
+
** 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]]
  
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
+
* 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]]
  
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.
+
* 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
  
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).
+
* 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
  
e) caltech needs to move their behinds and update their descriptions based on our omim data (will start prodding them after ws227)
+
* caltech needs to update their descriptions based on our omim data (will start asking them after ws227)
 +
** see above, info available
  
Optional f)
+
* Show phenotypes of connected genes on the disease pages, as they might be handy
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
  
And variant B)
+
* 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.
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
  
== Model ==  
+
== Model ==
== UI/test ==
+
* 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 ==  
 +
* providing development support as WB2 moves forward
 
== Tree_lister ==  
 
== Tree_lister ==  
== Search ==  
+
* 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 =  
 
= Position matrix data =  
== Data compile ==  
+
== Data compile ==
== Documentation ==  
+
* 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  =
 
= Miscellaneous UIs  =

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