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Table 7 Best parameters for optimizing performance for precision or recall

From: Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

High precision annotations
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model STRICT searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch SENSITIVE
stopWords ANY wordOrder ORDER MATTERS stemmer NONE
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize THREE/FIVE derivationalVariants NONE orderIndLookup OFF
withSynonyms NO scoreFilter 1000 findAllMatches NO
   minTermSize 3/5 synonyms EXACT ONLY
High recall annotations
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly NO model RELAXED searchStrategy SKIP ANY/ALLOW
filterNumber ANY gaps ALLOW caseMatch IGNORE/INSENSITIVE
stopWords ANY wordOrder IGNORE stemmer Porter/BioLemmatizer
SWCaseSensitive ANY acronymAbb ALL stopWords PubMed
minTermSize ONE/THREE derivationalVariants ALL/ADJ NOUN orderIndLookup ON
withSynonyms YES scoreFilter 0 findAllMatches YES
   minTermSize 1/3 synonyms ALL
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