Updating ontology (.obo) files for the OA

This information is for updating the object names obo files used for the phenotype OA a well as other OA interfaces.

In the Phenotype OA, all object fields, except strain should be autocomplete drop down lists. The files that are used to populate these fields are an obo-like format in that there is information attached to each object that shows up in the term info box when selected. Keeping the file updated from acedb and showing this information in the term info box helps during curation as it verifies the identity of the object being curated and saves the curator time from having to manually look up and verify the info themselves. These files although not technically 'obo files' will be referred to as obo files when referring to any flat file that contains a list of terms with accompanying information for display in the term info window. This is in contrast to other flat files that only contain a simple list of terms.

obo files for the phenotype OA

The following fields use an obo file, the name, source and script that generates the obo file used is noted.

• Pub field -> paper.obo
• Person field
• Variation ->obo_oa_ontology
• Transgene ->obo_oa_ontology
• Rearrangement ->obo_oa_ontology
• Caused by -> WBGene
• Phenotype ->phenotype.obo
• Molecule ->molecule.obo
• Anatomy ->WBbt.obo
• Life stage ->worm_development.obo
• Child of ->phenotype.obo
• Laboratory evidence
• Entity ->chebi.obo, rex.obo, gene_ontology_ext.obo
• Quality ->quality.obo

obo OA ontologies

This script : /home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl

Is on a cron job every day at 3am. It populates obo tables by downloading :

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/worm/worm_anatomy/WBbt.obo http://www.berkeleybop.org/ontologies/obo-all/worm_development/worm_development.obo http://www.berkeleybop.org/ontologies/obo-all/rex/rex.obo http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo (do we even use entity / quality in the phenotype OA ?) And it also calls :

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=AddToVariationObo

AQL Queries for updating the variation obo

Instructions for retrieving object connections from the latest WS build

Variation-gene, variation-paper connections are used to filter out the variation term drop down list to keep the size of the autocomplete file manageable. The total variation object class is filtered for those variations that are called 'alleles' or have a gene connection (which includes transposon variations). The files used for filtering this list need to be updated with each new release. To update this info, the following AQL queries need to be performed on the newest release and deposited on tazendra for the updating scripts.

Variation_gene connections

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. You will be making a file named Variation_gene.txt' that is a combination of vargene.txt and transposons.txt

• vargene.txt

select a, a->gene, a->gene->public_name, a->reference from a in class variation where exists_tag a->allele 
Export as vargene.txt  (choose Separator character set to blank (TAB))

• transposons.txt

select t, t->gene, t->gene->public_name, t>reference from t in class variation where exists_tag t->transposon_insertion and exists t->gene
Export as above as transposons.txt

• Make Variation_gene.txt by copying and pasting transposons.txt to the end of vargene.txt and saving as Variation_gene.txt"
• total_variations.txt

select v, v->gene, v->gene->public_name, v->reference from v in class variation
Export as total_variations.txt as above

//This is required for building an exclusion list that filters out SNPs, and is referred to as a junk list

Transgene_summary_paper connections

List transgenes already linked to a paper

• transpapsum.txt

select t, t->reference, t->summary from t in class transgene where exists t->reference
Export as transpapsum.txt  

Rearrangement_inside_gene connections

List rearrangements with LG, 'genes inside' and ‘gene outside’ (public names only)

• rearragene.txt

select r, r->map, r->gene_inside->public_name, r->gene_outside->public_name from r in class rearrangement
Export as rearragene.txt 

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Repopulating .obo's

Two scripts run off of these files to update the .obo's for the OA. 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

scp all files to acedb@tazendra.caltech.edu:/home/acedb/jolene/WS_AQL_queries

Scripts for repopulating the OA obo files

• Repopulates the OA autocomplete file, which is a full rewrite of the tables= >50 minutes. This script runs on a cron job at 3am every morning and shouldn't be run manually if you can help it. http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo

• 'on-the-fly' update to the variation list (quick <40 sec) http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=AddToVariationObo Launch this script to add variations that were recently created on the variation name server.

• Cron job: populate_newobjects_cgi_postgres_tables.pl updates information based on Variation_gene.txt and transgene_summary.txt. This script is required for posting new allele and transgene entries on to the New objects cgi and sending notifications to the relevant curators. (Make sure files are named accordingly or the program won’t see them).

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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.

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--kjy