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Table 3 Best performing parameter combinations for CL and GO subsections

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

Cell Type Ontology (CL)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model ANY searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch INSENSITIVE
stopWords ANY wordOrder ORDER MATTERS stemmer Porter/BioLemmatizer
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize ONE/THREE derivationalVariants ALL orderIndLookup OFF
withSynonyms YES scoreFilter 0 findAllMatches NO
   minTermSize 1/3 synonyms EXACT ONLY
Gene Ontology - Cellular Component (GO_CC)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model ANY searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch INSENSITIVE
stopWords ANY wordOrder ORDER MATTERS stemmer Porter
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize ONE/THREE derivationalVariants ANY orderIndLookup OFF
withSynonyms ANY scoreFilter 0/600 findAllMatches NO
   minTermSize 1/3 synonyms EXACT ONLY
Gene Ontology - Molecular Function (GO_MF)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly NO model ANY searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch ANY
stopWords ANY wordOrder ORDER MATTERS stemmer BioLemmatizer
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize ANY derivationalVariants ANY orderIndLookup OFF
withSynonyms NO scoreFilter 0/600 findAllMatches NO
   minTermSize 1/3 synonyms EXACT ONLY
Gene Ontology - Biological Process (GO_BP)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model ANY searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch INSENSITIVE
stopWords ANY wordOrder ORDER MATTERS stemmer Porter
SWCaseSensitive ANY acronymAbb ANY stopWords NONE
minTermSize ANY derivationalVariants ADJ NOUN VARS orderIndLookup OFF
withSynonyms YES scoreFilter 0 findAllMatches NO
   minTermSize 5 synonyms ALL
  1. Suggested parameters to use that correspond to best score on CRAFT. Parameters where choices don’t seem to make a difference in performance are represented as “ANY”.
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