Difference between revisions of "NBC sign off documentation"
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== UI == | == UI == | ||
* providing development support as WB2 moves forward | * providing development support as WB2 moves forward | ||
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= Ontology = | = Ontology = | ||
== Model == | == Model == | ||
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== Data compile == | == Data compile == | ||
* developing module for pipeline | * developing module for pipeline | ||
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+ | * 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 == | == Documentation == |
Latest revision as of 20:22, 29 July 2011
Contents
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