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KarrLab / datanator_rest_api

A OAS3 compliant REST API for the Datanator integrated database
MIT License
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Reaction full text search results include reactions with no data #90

Open jonrkarr opened 4 years ago

jonrkarr commented 4 years ago

Example:

lzy7071 commented 4 years ago

I am not too sure what it means but here's what I did to replicate the isssue:

If you were referring to Km or kcat, the has_poi (meaning has parameters, or rate constants, of interest) indicates if reactions have parameter information Km or kcat`. But I think we should return all reactions in the result, regardless of if it has rate constant information or not.

jonrkarr commented 4 years ago

I was referring to search results for trehalose: https://datanator.info/search/trehalose/.

Of the top 10 reaction results, 6 of the links point to pages which don't display any data. Examples:

jonrkarr commented 4 years ago

The issue was that the search results include parameters that the frontend doesn't understand. I fixed most of the cases by extending the front end to support K_I (inhibitory constants) and parameters that use non-canonical units (by adding separate columns for units).

With my changes, the above errors are not longer relevant. Ignore the message above.

We still need to make 1 change to the reaction full text search. The full text search should only cover parameters with the following type or sbo_type:

jonrkarr commented 4 years ago

Similar to #86 and #89, upon further reflection, I think its useful for Datanator explicitly communicate the absence of relevant data.

When we have more time, lets add an option to only return reactions that have kinetic measurements -- at least one parameter with (a) value or observed_value != null and (b) type or sbo_type is equal one of the following: