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Inconsistent data type for `biolink:supporting_text`

Open isbluis opened this issue 3 months ago • 4 comments

The biolink:supporting_text attribute seems to have a value of type object/dict in rtx-kg2, but list/array in ARAX

Business impact: this may cause an issue for tools that parse these results downstream, with a likely outcome of not displaying to the user the supporting text from the publication presented as evidence for a given edge / relationship. Anecdotal evidence suggests that this is already happening in production.

  • Example of data represented as a list of dicts: https://arax.ncats.io/?r=354684 :: See result 1 → Analysis support graph → edge (with primary_knowledge_source = infores:arax ) Image

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  • Example of data represented as a dict: https://arax.ncats.io/?r=355183 :: See result 1 → any edge (with primary_knowledge_source = infores:semmeddb, and aggregator_knowledge_source = infores:rtx-kg2) Image

isbluis avatar Sep 24 '25 23:09 isbluis

@Genomewide @webyrd do you know which the UI prefers? A list or an object/dict?

dkoslicki avatar Sep 25 '25 02:09 dkoslicki

I think these lines make it as an array/list of object. So, if we prefer an object/dict, just need to update these lines.

chunyuma avatar Sep 25 '25 04:09 chunyuma

I see those lines turning it into a list; is the thought process that if these attributes already exist as a dict they would just stay as a dict?

dkoslicki avatar Sep 25 '25 12:09 dkoslicki

I think the answer is yes. I didn't see that there are other places that turn them into a list except for these lines.

chunyuma avatar Sep 25 '25 14:09 chunyuma