Updating ontology (.obo) files for the OA
Contents
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 /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
Transgene_summary_paper connections
To: List transgenes already linked to a paper
Run the following AQL: select t, t->reference, t->summary from t in class transgene where exists t->reference
- Sort results (optional)
- Export as WS#_transpapsum into /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
Rearrangement_inside_gene connections
To: List rearrangements with LG, 'genes inside' and ‘gene outside’ (public names only)
Run the following AQL: select r, r->map, r->gene_inside->public_name, r->gene_outside->public_name from r in class rearrangement
- Sort results (optional)
- Export as WS#_rearragene into /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
Repopulating Postgres
Two scripts 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. The scripts are on tazendra and run off of files Variation_gene.txt, transgene_summary_reference.txt and rearr_simple.txt. So files need to be transferred to tazendra and renamed to be recognizable by those scripts.
Transfer files to tazendra
Scripts are stored in 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 rearr_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
Scripts to populate Phenote .obo files
- 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.
Both apps are on tazendra in the same directory as the updated variation info.
cd to /home/acedb/karen/populate_gin_variation/ $ ./populate_ali_alleleinfo.pl $ ./ make_obo.pl
NOTE: populate_gin_variation updates data based on variation_tab_wbgene file (in postgres / cgi) , which is no longer current.
To check if the re-population scripts worked, check out the WS_current info field The date will tell you when it was last updated; it should reflect the date the script was run.
--kjy