Difference between revisions of "Updating ontology (.obo) files for the OA"
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====Allele_gene connections==== | ====Allele_gene connections==== | ||
− | + | ''List all variations in the allele group (and not polymorphisms) that exist in the database and where it is known, the gene it has been assigned to.'' | |
− | (AQL) select g, g->gene, g->gene->public_name from g in class variation where exists_tag g-> allele | + | |
+ | (AQL) | ||
+ | select g, g->gene, g->gene->public_name from g in class variation where exists_tag g-> allele | ||
+ | |||
+ | Sort (optional) | ||
+ | Export as WS#_vargene into folder Phenote on local desktop (choose Separator character set to blank (TAB)) | ||
+ | |||
+ | ====Transgene_summary_paper connections==== | ||
+ | ''List transgenes and linked paper'' | ||
+ | |||
+ | (AQL) | ||
+ | select t, t->reference, t->summary from t in class transgene where exists t->reference | ||
Sort (optional), | Sort (optional), | ||
− | Export (choose Separator character set to blank (TAB)) | + | Export as WS#_transpapsum into folder Phenote on Desktop (choose Separator character set to blank (TAB)) |
+ | |||
+ | ====Rearrangement_inside_gene connections==== | ||
+ | ''List rearrangements with LG, 'genes inside' and ‘gene outside’ (public names only)'' | ||
− | + | (AQL) | |
− | + | select r, r->map, r->gene_inside->public_name, r->gene_outside->public_name from r in class rearrangement | |
− | (AQL) select | + | Sort (optional) |
− | Sort (optional) | + | Export as WS#_rearragene into folder Phenote on Desktop (choose Separator character set to blank (TAB)) |
− | Export (choose Separator character set to blank (TAB)) | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | Repopulating Postgres | + | ===Repopulating Postgres=== |
Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation | Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation | ||
− | + | Rename WS188_vargene.txt to Variation_gene.txt | |
− | $scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt | + | $scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt |
− | + | Rename WS188_rearragene.txt to rear_simple.txt | |
− | $scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt | + | $scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt |
− | + | Rename WS188_transpapsum to transgene_summary_reference.txt | |
− | $scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt | + | $scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt |
Running scripts to populate Phenote .obo files | Running scripts to populate Phenote .obo files |
Revision as of 21:55, 13 March 2008
Contents
Updating .obo files
Populating Postgres with object connections from the latest build files
Variation-gene and variation-paper connection information retrieved in phenote depends on information from the latest WS. After the upload, these .obo files in Postgres need to be repopulated with the most current information.
Run queries on the latest WS release for the most current information (it probably matters that the queries maintain the same column output?)
Allele_gene connections
List all variations in the allele group (and not polymorphisms) that exist in the database and where it is known, the gene it has been assigned to.
(AQL) select g, g->gene, g->gene->public_name from g in class variation where exists_tag g-> allele
Sort (optional) Export as WS#_vargene into folder Phenote on local desktop (choose Separator character set to blank (TAB))
Transgene_summary_paper connections
List transgenes and linked paper
(AQL) select t, t->reference, t->summary from t in class transgene where exists t->reference Sort (optional), Export as WS#_transpapsum into folder Phenote on Desktop (choose Separator character set to blank (TAB))
Rearrangement_inside_gene connections
List rearrangements with LG, 'genes inside' and ‘gene outside’ (public names only)
(AQL) select r, r->map, r->gene_inside->public_name, r->gene_outside->public_name from r in class rearrangement Sort (optional) Export as WS#_rearragene into folder Phenote on Desktop (choose Separator character set to blank (TAB))
Repopulating Postgres
Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation
Rename WS188_vargene.txt to Variation_gene.txt
$scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt
Rename WS188_rearragene.txt to rear_simple.txt
$scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt
Rename WS188_transpapsum to transgene_summary_reference.txt
$scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt
Running scripts to populate Phenote .obo files There are two scripts, populate_ali_alleleinfo.pl and make_obo.pl that need to be run to populate Postgres with the updated variation information. It is important to run these scripts every time the variation information is updated. Both apps are on tazendra in the same directory as the updated variation info. Run scripts: cd to /home/acedb/karen/populate_gin_variation/ $ ./populate_ali_alleleinfo.pl $ ./ make_obo.pl
populate_ali_alleleinfo.pl updates information based on Variation_gene.txt and transgene_summary_reference.txt. Make sure files are named accordingly or the program won’t see them.
make_obo.pl creates a text .obo based on rearr_simple.txt and Variation_gene.txt. This script populates the WS current info.
NOTE: populate_gin_variation updates data based on variation_tab_wbgene file (in postgres / cgi) , which is no longer current.
To check if the repopulation scripts worked, check out the ws current info field http://tazendra.caltech.edu/~azurebrd/var/work/phenote/ws_current.obo The date will tell you when it was last updated; it should reflect the date the script was run.
--kjy