smartAPI icon indicating copy to clipboard operation
smartAPI copied to clipboard

Support metakg queries with biolink model's semantic descendants

Open newgene opened this issue 2 years ago • 1 comments

Each edge in SmartAPI's metakg contains subject, object, predicate fields which are the terms based on the biolink model. We should add the metakg query support for searching on either of these fields by optionally expanding to include all descendant terms.

We can use biolink-model-toolkit to get the descendant of a given term.

In metakg's query handler, we can add explicit subject, object and predicate query parameters, and an optional expand parameter when can take values of subject, object and predicate (include their combinations), so that we can expand either or multiple fields when needed. Default is still not expanding these terms.

newgene avatar Mar 07 '23 06:03 newgene

This is pending on the completion of #179

newgene avatar Mar 07 '23 06:03 newgene

@newgene Is this related to the &expand option we added to the metakg and pathfinder?

NikkiBytes avatar Sep 26 '24 20:09 NikkiBytes

@NikkiBytes yes, maybe you can add a brief usage comment of this expand parameter and then we can close this one.

newgene avatar Sep 26 '24 20:09 newgene

Implemented feature in /metakg and and /metakg/paths endpoint, with &expand= option. Currently it accepts 1 or more of the options: subject, object, predicate, node, edge, or all.
i.e https://smart-api.info/api/metakg/?subject=BiologicalEntity&object=BiologicalEntity&expand=subject

To view a summary of the terms that were found when expanded, use &rawquery=1: https://smart-api.info/api/metakg/?subject=BiologicalEntity&object=BiologicalEntity&expand=subject&rawquery=1

NikkiBytes avatar Sep 26 '24 22:09 NikkiBytes