Workflow B: SemMedDB "Novelty" constraint

[karafecho]

This issue is to follow up on Andrew Su's suggestion to consider ways to leverage SemMedDB's "Novelty" constraint by setting it to Novelty=0 either in the query itself or via another approach.

[andrewsu]

Just some quick notes about how we can check whether this is likely to have much/any impact before we actually write any additional code.

I believe the issue to be addressed can be seen in the ARAX response for Query B.1. The observation is that many non-specific nodes (e.g., "cytokine", "MicroRNAs", "agonists") are appearing in the results. The hypothesis is that filtering on "novelty" node property in SemmedDB (eliminating nodes where novelty = 0) would enrich for results that SMEs would care about.

The Service Provider has created a new API for semmeddb that includes the novelty score at https://biothings.ncats.io/semmeddb. So let's check a few of the B.1 results to see what their novelty scores are:

• cytokine: ARAX reports that to be FMA:84050, which synonym matcher says is UMLS:C0079189, which can be searched using https://biothings.ncats.io/semmeddb/query?q=subject.umls:C0079189%20OR%20object.umls:C0079189, which says novelty: 1. So novelty would not be helpful in eliminating "cytokine"
• MicroRNAs": MESH:D035683 -> UMLS:C1101610 -> https://biothings.ncats.io/semmeddb/query?q=subject.umls:C1101610%20OR%20object.umls:C1101610 -> novelty: 1
• agonists: MESH:Q000819 -> UMLS:C0243192 -> https://biothings.ncats.io/semmeddb/query?q=subject.umls:C0243192%20OR%20object.umls:C0243192 -> novelty:0

I hope I've illustrated how the semmeddb novelty score currently can be accessed. Perhaps a SME or analyst with workflow B could do more spot checking on the nodes they would consider to be "too generic"?