Updating ontology (.obo) files for the OA

This obo file is used to display term info for variations, transgenes, strains, clones, rearrangements, genes in any OA interface that contains these objects. It needs to be updated with every release of acedb. The obo file is created from AQL queries of the latest WS.

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_name_variation; obo_data_variation
  
• Transgene ->trp tables
• 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

See Ontology update pipeline here for variation, clone, strain, rearrangement, and laboratory obo table, basically these files are updated from a nightly geneace dump.
Transgenes should be updated directly from the trp tables.
Variations are also updated from the

All other ontologies in the phenotype OA should be updated through the following script:

/home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl

obo tables are populated by downloading :

Phenotype term: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi
Molecule ChEBI: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo
Gene ontology: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
Anatomy: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/worm/worm_anatomy/WBbt.obo
Life stage: http://www.berkeleybop.org/ontologies/obo-all/worm_development/worm_development.obo
Pathogen: h_pap_species_index PATO entity: http://www.berkeleybop.org/ontologies/obo-all/rex/rex.obo
PATO quality: http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo
NOTE: Across all ontologies all "is_obsolete: true" are changed to be red.

Everyday this script calls and incremental update from the variation nameserver:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo 
Note: this was changed from http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=AddToVariationObo

On the 1st of the month the script calls a full variation obo update:

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

--kjy 22:33, 4 September 2013 (UTC)

Repopulating variation OA obo from geneace

For each variation with specific Method (listed in table below), the following information will be retrieved:

• WBVar ID
• public_name
• gene association
• references
• method
• status

Only variations with one of the following attached methods are retrieved. 
   Allele
   Deletion_allele
   Deletion_and_insertion_allele
   Deletion_polymorphism
   Insertion_allele
   Insertion_polymorhism
   KO_consortium_allele
   Mos_insertion
   NBP_knockout_allele
   NemaGENETAG_consortium_allele
   Substitution_allele
   Transposon_insertion
   Engineered_allele

These data will populate /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace files
obo_name_variation
obo_data_variation

in obo_name_variation, entries are like:

WBVar00000020	ad487	2015-11-30 20:01:08

in obo_data_variation, entries are like:

WBVar00088136	id: WBVar00088136\nname: "ju2"\nspecies: "Caenorhabditis elegans"\nstatus: "Live"\ngene: "WBGene00006363 syd-1"\nreference: "WBPaper00005543"	2015-11-30 20:01:08

If a variation does not exist in the geneace dump, and hence not in obo_name/data_variation tables

• retrieve a WBVarID from the variation nameserver at http://www.sanger.ac.uk/sanger/Worm_NameServer (you will need a login and password, which may take a while to be assigned)
• enter the public name and WBVarId, separated by a space OR tab, into the TempVariationObo http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo * * note: The form can take columns of data as long as it is in the format of <allele public name> <WBVarID>.

The information is added immediately to the obo_name_variation and should be available through the OA variation field (a form reload may be necessary).

If the allele already has a WBVarID but does not exist in the nightly geneace dump, curators should still enter the object through the generic.cgi. (http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo)
When the object comes through during the geneace dump, its information will be captured and overwritten in obo_data_variation.
For variations that already exist in geneace but do not come through the geneace dump, e.g., million mutation varations, etc., they will remain in obo_data_variation and still be available through the drop down.

If a variation needs correcting, go to /home/azurebrd/public_html/cgi-bin/data/obo_tempfile_variation and you can manually edit the file. --Kyook (talk) 20:01, 29 September 2017 (UTC)

Obsolete

Obsolete-> 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.

Obsolete -> Updating variation obo This script looks at the files in:

home/acedb/jolene/WS_AQL_queries
  Variation_gene.txt
  total_variations.txt
  clone_info.txt
  strains.txt
  rearr_simple.txt
  expr_cluster.txt

and the new Gene Class file to

populate the obo_*_geneclass tables.

To launch the full update manually log in to tazendra as acedb and do

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

Because it takes so long, make sure to wait until people do not require the ontologies to work in the OA.

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-obsolete) 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

Obsolete ->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 or 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).

Obsolete ->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 Grab latest build from spica.

Variation-gene, variation-paper connections are used to select for variations of type allele or those that affect CDS (can include transposon and polymorphism alleles). This is necessary to keep the size of the variation autocomplete file manageable and not slow down the loading and using of the OA.

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 a from a in class variation where exists a->variation_type\\
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

• transgene_summary.txt

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

Rearrangement_inside_gene connections

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

• rearr_simple.txt

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

Strain info

Added 5.17.11 for Daniela

• strains.txt

select s, s->genotype, s->location from s in class strain

Clone info

Added 5.17.11 for Daniela

• clone_info.txt

select a, a->Type, a->transgene, a->strain, a->general_remark, a->location, a->accession_number, a->reference from a in class clone

---

back

--kjy

/home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl