Listing the common biological entites, which glida fails to normalize

[Crispae]

Raw	Glida Normalized	Correct
AD	ADIPOQ (hgnc:13633)	Alzheimer Disease (mesh:D000544)

[Crispae]

Also need to add column with context.

[bgyori]

Hi Crispae, thanks for reporting this, however, this looks like a misunderstanding. "AD" is a highly ambiguous string and it is not possible to determine its sense without additional context.

Actually, Gilda does return both hgnc:13633 and mesh:D000544 in its list of matches for "AD" which is the expected behavior:

In [3]: gilda.ground('AD')
Out[3]: 
[ScoredMatch(Term(ad,AD,HGNC,13633,ADIPOQ,synonym,adeft,None,None,None),0.5555555555555556,Match(query=AD,ref=AD,exact=True,space_mismatch=False,dash_mismatches={},cap_combos=[])),
 ...
ScoredMatch(Term(ad,AD,MESH,D000544,Alzheimer Disease,synonym,adeft,None,None,None),0.5555555555555556,Match(query=AD,ref=AD,exact=True,space_mismatch=False,dash_mismatches={},cap_combos=[])),
 ...

if I provide meaningful additional context, Gilda can detect that the correct sense in that particular context is Alzheimer Disease:

In [7]: gilda.ground('AD', 'AD is a neurodegenrative disease and it is associated with Abeta accumulation.')
INFO: [2023-11-05 18:02:16] gilda.grounder - Running Adeft disambiguation for AD
Out[7]: 
[ScoredMatch(Term(ad,AD,MESH,D000544,Alzheimer Disease,synonym,adeft,None,None,None),0.5555485494219966,Match(query=AD,ref=AD,exact=True,space_mismatch=False,dash_mismatches={},cap_combos=[]),disambiguation={"type": "adeft", "score": 0.9999873889595938, "match": "grounded"}),

[Crispae]

Hi Thanks for response, Yes I check that, it can disambiguate. I was wondering to add some more terms related to specific use case. I went through the tutorial, but for each list of term we need to build different grounder, is there anyway we can merge those terms with default terms already merged with glida, so it can ground entity with whole terms list, not from specific list of terms.

Thanks