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./metamaplite.sh --chemdnersldi input_file.txt
This returns
unknown option: --chemdnersldi
Content of input_file.txt
1|'Heart Attack' 2|'John had a huge heart attack'
Update: After going through the source code: https://github.com/lhncbc/metamaplite/blob/master/src/main/java/gov/nih/nlm/nls/ner/MetaMapLite.java
found that I should be using the command: ./metamaplite.sh --inputformat=sldiwi input_file.txt
I was wrong in assuming that I should be using chemdnersldi. SingleLineDelimitedInputWithID should be the document input format.
The text was updated successfully, but these errors were encountered:
@willjrogers For the above two sentences in input file, following is the output:
ConceptLiteMMI(index='1', mm='MMI', score='0.52', preferred_name='Attack behavior', cui='C1261512', semtypes='[socb]', trigger='"attack"-text-0-"Attack"-NNP-0', pos_info='7/6', tree_codes='') ConceptLiteMMI(index='1', mm='MMI', score='0.52', preferred_name='Observation of attack', cui='C1304680', semtypes='[fndg]', trigger='"Attack"-text-0-"Attack"-NNP-0', pos_info='7/6', tree_codes='') ConceptLiteMMI(index='1', mm='MMI', score='0.52', preferred_name='Onset of illness', cui='C0277793', semtypes='[tmco]', trigger='"Attack"-text-0-"Attack"-NNP-0', pos_info='7/6', tree_codes='') ConceptLiteMMI(index='2', mm='MMI', score='3.75', preferred_name='Myocardial Infarction', cui='C0027051', semtypes='[dsyn]', trigger='"Heart Attack"-text-0-"heart attack"-NN-0', pos_info='17/12', tree_codes='C14.280.647.500;C14.907.585.500')
Sentence 1 fails to give the concept: 'Myocardial Infarction' This might be a bug in MetaMapLite.
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./metamaplite.sh --chemdnersldi input_file.txt
This returns
Content of input_file.txt
1|'Heart Attack'
2|'John had a huge heart attack'
Update:
After going through the source code: https://github.com/lhncbc/metamaplite/blob/master/src/main/java/gov/nih/nlm/nls/ner/MetaMapLite.java
found that I should be using the command:
./metamaplite.sh --inputformat=sldiwi input_file.txt
I was wrong in assuming that I should be using chemdnersldi.
SingleLineDelimitedInputWithID should be the document input format.
The text was updated successfully, but these errors were encountered: