Ticket #191 (assigned enhancement)

Opened 3 years ago

Last modified 3 years ago

Include searchable Xrefs in Ontology terms (bv CAS for CHEBI)

Reported by: e.vansomeren@… Owned by: business@…
Priority: minor Milestone: Should have
Component: General Version:
Keywords: Cc:
Product: Operating system:
URL: Hardware:

Description

CAS nr are a commonly used ID for compounds. So when looking for a compound, the user should be able to fill in CAS nr as well, rather than only names or synonyms which is currently the case. In CHEBI.obo I found that CAS nr are connected to compounds as an Xref field.

So, in general, this could be fixed by simply including Xrefs when searching for any ontology term.

Change History

follow-up: ↓ 2   Changed 3 years ago by business@…

Indeed CAS numbers are stored as Xref in CHEBI (ChemIDplus), see e.g. [ http://bioportal.bioontology.org/visualize/44746/?conceptid=CHEBI%3A39106&jump_to_nav=true
here]. Also, from  this documentation it is clear that BioPortal? returns 'relations' in the XML for a Term which probably also would contain ChemIDplus for CHEBI.
So technically this should be possible. However, how this fits into the general template structure / ontology term fields in GSCF remains a question. It would be possible to store all Xrefs with each terms, but this might be overkill. We could also add a list of 'xref ids' for each ontology template field, which would result in interesting xref fields that will be exported when available, so that when a user chooses to export an entity with ontology fields, those xrefs would be supplied as extra fields (e.g. columns in the Excel export). Thoughts on this are welcome!

in reply to: ↑ 1   Changed 3 years ago by business@…

Replying to business@…:

so that when a user chooses to export an entity with ontology fields, those xrefs would be supplied as extra fields (e.g. columns in the Excel export)

I mean that in that case the exporter should dynamically retrieve the terms from BioPortal? at runtime and lookup the Xrefs.

  Changed 3 years ago by work@…

I assume you mean the importer, not the exporter...

  Changed 3 years ago by work@…

  • owner set to business@…
  • status changed from new to assigned
  • milestone set to 0.7

  Changed 3 years ago by business@…

I actually meant the (SimpleTox? or generic Excel) exporter, and also probably the study overview.

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