Updating ontology (.obo) files for the OA

Updating .obo files

Retrieving 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

To: Find all variations in the allele group (excludes SNPs etc.) along with the WBGeneID and public gene name of the gene they are assigned, if that is available.

Run the following AQL:  
select g, g->gene, g->gene->public_name from g in class variation where exists_tag g-> allele 

Sort results (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.

back

--kjy