Detecting negation for one CUI but failing to detect negation for other CUIs about negbio

[yfpeng]

negbio cannot handle this case right now because it should be "spinal canal hematoma" not just "spinal" to be recognized as C0856150. It is an error produced by MetaMap. An alternative way is creating a dictionary that contains "spinal canal hematoma" and then using the chexpert labeler to recognize it.

Please see https://negbio.readthedocs.io/en/latest/user_guide.html#named-entity-recognition

[kaushikacharya]

Hi @yfpeng
I checked the output of MetaMap and found that the issue is in NegBio.
There are four different ways of Positional Information as mentioned in Metamap documentation.

https://github.com/ncbi-nlp/NegBio/blob/master/negbio/pipeline/dner_mm.py#L58

m = re.match(r'(\d+)/(\d+)', concept.pos_info)

Here we are only handling the 1st type i.e. the simplest form where the concept's text is a contiguous block of characters.

Here's the output of pyMetaMap for the example case in this issue:

ConceptMMI(index='1', mm='MMI', score='16.15', preferred_name='Spinal Canal', cui='C0037922', semtypes='[bsoj]', trigger='["Spinal Canal"-tx-1-"spinal canal"-noun-0]', location='TX', pos_info='13/12', tree_codes='A02.835.232.834.803')

ConceptMMI(index='1', mm='MMI', score='16.09', preferred_name='Pulp Canals', cui='C0086881', semtypes='[bsoj]', trigger='["Canal"-tx-1-"canal"-noun-0]', location='TX', pos_info='20/5', tree_codes='A14.549.167.900.265')

ConceptMMI(index='1', mm='MMI', score='13.09', preferred_name='Hematoma', cui='C0018944', semtypes='[patf]', trigger='["HEMATOMA"-tx-1-"hematoma"-noun-1]', location='TX', pos_info='26/8', tree_codes='C23.550.414.838')

ConceptMMI(index='1', mm='MMI', score='3.78', preferred_name='spinal hematoma', cui='C0856150', semtypes='[inpo]', trigger='["spinal hematoma"-tx-1-"spinal hematoma"-noun-1]', location='TX', pos_info='13/6,26/8', tree_codes='')

ConceptMMI(index='1', mm='MMI', score='3.63', preferred_name='Hematoma Adverse Event', cui='C1962958', semtypes='[fndg]', trigger='["Hematoma"-tx-1-"hematoma"-noun-1]', location='TX', pos_info='26/8', tree_codes='')

ConceptMMI(index='1', mm='MMI', score='3.48', preferred_name='Body Parts - Canal', cui='C1550227', semtypes='[bpoc]', trigger='["Canal"-tx-1-"canal"-noun-0]', location='TX', pos_info='20/5', tree_codes='')

ConceptMMI(index='1', mm='MMI', score='3.48', preferred_name='Geographic canal', cui='C0442636', semtypes='[geoa]', trigger='["Canal"-tx-1-"canal"-noun-0]', location='TX', pos_info='20/5', tree_codes='')

The spinal hematoma concept [Positional Information: (13/6,26/8)] is of type (b) of positional information i.e. disjoint text strings.
Currently in the NegBio code, re.match() is only returning the 1st match.