Set of ontologies for lookup

[mikkonie]

We need to set up an initial set of supported ontologies when deploying the ontology editor feature of #699.

My thinking is to query for existing sheets on sodar.bihealth.org and collect a list from there. I'll have to test each ontology to make sure they work correctly with the parser.

The Ansible playbook will also have to be edited to import/update the ontologies using the importobo management command.

TL;DR

• OK: CL, DUO, HP, MS, OBI, OMIM, ORDO, PATO, PRIDE, ROLEO, UBERON
• NOT OK: ICD10, MESH, SNOMEDCT
• Unknown: CLO

Currently Used in CUBI SODAR

• CL: OK
• CLO: TODO (What is this? Same as CL?)
• DUO: OK
  • Only 37 terms imported after conversion?
• HP: OK
• ICD10: NOT OK
  • Needs some bioportal API key to download?
• MESH: NOT OK
  • Not available in any supported format
• MS: OK
• NCBITAXON: OK
  • Using slim version
• OBI: OK
  • Contains a lot of references to terms from other ontologies, should be parsed last
• OMIM: OK
  • Special parsing implemented
• ORDO: OK
  • Requires fixes version (see below)
• PATO: OK
• PRIDE: OK
  • Requires a fixed version (see below)
• ROLEO: OK
• SNOMEDCT: NOT OK
  • Invalid OWL: could not findowl:Ontologyelement
• UBERON
  • Requires fixes or a better version (see below)
• UO: TODO
  • Unit ontologies not currently supported

Currently Not Used

• GO

TBD: Are these needed?

Fixed

• UBERON
  • expected QuotedString (<stdin>, line 188908)
  • This one is full of errors not accepted by this browser
    • Not sure if this is a proper version to use?
  • Fixed version here
• ORDO
  • expected EOL or QuotedString (<stdin>, line 21)
  • Errors caused by xref tags towards SNOMED CT, which we are not currently using
  • Fix: Replace occurrences of SNOMED CT: with SNOMED_CT: (Edit: I guess SNOMEDCT is actually correct, but it's irrelevant as xrefs aren't used)
  • Fixed version here
• PRIDE
  • Fastobo exception: expected XrefList (<stdin>, line 80)
  • Full of errors, fortunately easy to fix
  • Fixed version here

Available But Not Working

N/A

Non-Standard Accession URL Patterns

• ORDO: http://www.orpha.net/ORDO/{id_space}_{local_id}
• PRIDE: ???
• ROLEO: ???

[mikkonie]

Django shell script to get currently used ontologies by name:

from samplesheets.models import Investigation
ol = []

for inv in Investigation.objects.all(): 
    for o in inv.ontology_source_refs: 
        if o['name'] not in ol: 
            ol.append(o['name'])

for o in sorted(ol):
    print(o)

[mikkonie]

Storing list of management commands for import here in lack of a better place.

./manage.py importobo -n CL --title "Cell Ontology" -u http://purl.obolibrary.org/obo/cl.obo
./manage.py importobo -n DUO --title "Data Use Ontology" -u http://purl.obolibrary.org/obo/duo.owl
./manage.py importobo -n HP --title "Human Phenotype Ontology" -u http://purl.obolibrary.org/obo/hp.obo
./manage.py importobo -n MS --title "Mass Spectrometry Ontology" -u http://purl.obolibrary.org/obo/ms.obo
./manage.py importobo -n NCBITAXON --title "NCBI Taxonomy" -u https://github.com/obophenotype/ncbitaxon/releases/download/current/taxslim.obo
./manage.py importobo -n ORDO --title "Orphanet Rare Disease Ontology" -p /LOCAL/PATH/orphanet_ordo_fix.obo --term-url "http://www.orpha.net/ORDO/{id_space}_{local_id}"
./manage.py importomim -p /LOCAL/PATH/OMIM.csv
./manage.py importobo -n PATO --title "Phenotype And Trait Ontology" -u http://purl.obolibrary.org/obo/pato.obo
./manage.py importobo -n PRIDE --title "PRoteomics IDEntifications" -p /LOCAL/PATH/pride_cv_fix.obo
./manage.py importobo -n ROLEO --title "Role Ontology" -u http://data.bioontology.org/ontologies/ROLEO/submissions/3/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb -f owl
./manage.py importobo -n UBERON --title "Uberon" -p /LOCAL/PATH/uberon_basic_fix.obo
./manage.py importobo -n OBI --title "Ontology for Biomedical Investigations" -u http://purl.obolibrary.org/obo/obi.obo

[mikkonie]

Update for current versions of ontologies and fastobo-py v0.10.1:

• CL: FAIL
  • Fastobo exception: expected Iso8601Year (<stdin>, line 164870)
• DUO: OK
• HP: OK
• MS: OK
• NCBITAXON: See below
  • URL = 404 not found!
  • Works with local file
• ORDO: OK
• OMIM: OK
• PATO: OK
• PRIDE: OK
• ROLEO: OK
• UBERON: OK
• OBI: OK