biovalidator: support for ontology versions

[theisuru]

elixir-europe/biovalidator#50

Currently biovalidator uses latest version of the ontology for valdation. It should extend support to ontology versions.

[theisuru]

OLS does not support ontology versions and only contains the latest version. Therefore this is not possible at the moment.
Only thing we can do is return ontology version used for validaton. But this require considerable modifications to the current model.

Email thread from OLS team

Hi Isuru,

Thank you for your kind wishes and Happy New Year to you too!

Unfortunately, we don't have any endpoint which serves versioned ontologies
because our data processing pipeline fetches the latest versions of the
ontologies and reindexes the data everytime it runs.

I hope this helps and please let me know if you need any further information.

Cheers,
Haider

 

On Fri Jan 03 11:25:14 2025, isuru wrote:

Dear OLS team,
Wishing you a wonderful start to the year!
We are using OLS /search endpoint to query for ontology terms in
biovalidator. Biovalidator validates if data is a child term of given
ontology with a set of restrictions. Currently when querying to check
available child terms, we restrict search using 'ontology' and
'allChildrenOf' filter parameters.
As I understand this  endpoint uses latest ontology version to support
these queries. We would like to use ontology versions when querying to
make sure we store version with validation results, so we can validate
data at a later stage. In your documentation I could not find any
information related to versions, particularly in /search endpoint.
Could you please let me know if /search endpoint supports versioning or
if there are any other endpoint that supports version related queries.
Thanks,
Isuru

[theisuru]

I am moving this to done as there is nothing we could do at this stage. This is tracked in biovalidator repo.
elixir-europe/biovalidator#50