Ticket #127 (closed enhancement: wontfix)

Opened 4 years ago

Last modified 3 years ago

take into account ontology versioning, make more use of Ontocat

Reported by: business@… Owned by:
Priority: major Milestone: Could have
Component: General Version:
Keywords: Cc:
Product: Operating system:
URL: Hardware:

Description (last modified by business@…) (diff)

Problem that originally raised versioning: When I click add more... to add more terms to the Compound ontology in the GSCF demo instance on demo.dbnp.org, the new compounds do not show up in the list afterwards. This works with a local installation.

  • Implement ontology versioning
  • Use Ontocat instead of going direct to BioPortal?, to be able to include more ontologies and also profit from other things done in Ontocat (e.g. when NCBO changes its webservices again)

Change History

Changed 4 years ago by business@…

  • milestone set to 0.5.1

Changed 3 years ago by work@…

This bug is caused by the Ontology being updated on the ncbo side. We already have one version in the database (1.71) which has only one term linked (glucose). When you tried to add other terms, these terms came from a newer version of the Ontology (1.72) which did not yet exist in the database so a new Ontology was created. The Terms benzo[a]pyrene, benzene and benzenediols were added to this Ontology.

The wizard -however- shows the terms of the first occurance of the Ontology, hence 'Glucose'.

Also, the glucose that is now in the database (CHEBI:17234, Ontology v 1.71) has the same identifier from the one in the 1.72 Ontology (CHEBI:17234) so at least that did not change.

I think the best resolution (for now?) would be to update the existing ontology to the newer version.

Changed 3 years ago by work@…

  • status changed from new to closed
  • resolution set to fixed

Resolved in svn #997.

Resolution: before adding a new ontology, a lookup is performed on name. If this returns an existing ontology, the existing ontology is updated with the updated information of the new version of the ontology. This solution is not ideal, but good enough for now...

As I also explained (in inline-comments) in the TermEditorController?:

// this is a newer version of an existing Ontology, update
// the ontology to a newer version. This is not the best
// way to handle these updates as we don't know if terms
// have been updated. However, introducing different versions
// of Ontologies results into numerous difficulties as well:
// - what to do with studies that rely on an older ontology
// - when a new ontology is added, the existing terms of the
// older version are lacking in the new version
// - the webservice can only search on ontologyid, not on
// versions of ncboVersioned id's
// - if the name has changed between versions this check
// will not work anymore
// - etc :)
// So for now, we will just update the existing ontology with
// the new information until it becomes clear this needs a
// more thorough workaround...

Changed 3 years ago by business@…

  • priority changed from blocker to major
  • component changed from Study create/edit wizard to GSCF in general
  • summary changed from added ontology terms (e.g. compound benzo[a]pyrene) with add more... do not show up to take into account ontology versioning, make more use of Ontocat
  • type changed from defect to enhancement
  • milestone changed from 0.5.1 to 0.8

@Jeroen: maybe we should also enforce on domain class level that only 1 Ontology entry with a certain ncboId can exist for now, just to make sure this bug does not turn up anywhere?

Also, assigned this ticket to a later milestone and made it more general. Together with the versioning, we could think about making more use of Ontocat, to allow not only BioPortal? ontologies but also OLS and local ontologies. The latter is important to be able to add e.g. a 'placebo' term to ChEBI, which is not a chemical compound in itself but still should be in the list of compounds.

Changed 3 years ago by business@…

  • status changed from closed to reopened
  • resolution fixed deleted

Changed 3 years ago by business@…

  • description modified (diff)

Changed 3 years ago by business@…

  • description modified (diff)

Changed 3 years ago by work@…

closing issue as we don't seem to be having any ontology issues at the moment... let's raise another issue _if_ we encounter new issues in the future...

Also, using NCBO portal directly instead of going Ontocat obviously is faster

Changed 3 years ago by work@…

  • status changed from reopened to closed
  • resolution set to wontfix
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