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 -- /usr/local/wormbase/databases/ | + | ** 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]] | ** 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 | * 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/ | + | ** 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]] | ** 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 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). | |
+ | ** 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, but then who cares. | |
+ | ** caltech issue | ||
− | + | * caltech needs to move their behinds and update their descriptions based on our omim data (will start prodding them after ws227) | |
+ | ** see above, info available | ||
− | + | * 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 |
− | + | * 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) | |
− | 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 == |
Revision as of 17:55, 20 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 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).
- 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, but then who cares.
- caltech issue
- caltech needs to move their behinds and update their descriptions based on our omim data (will start prodding 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 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