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Table 4 Best performing parameter combinations for SO, ChEBI, NCBITaxon, and PRO

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

Sequence Ontology (SO)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model STRICT searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch INSENSITIVE
stopWords ANY wordOrder ANY stemmer Porter/BioLemmatizer
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize THREE derivationalVariants NONE orderIndLookup OFF
withSynonyms YES scoreFilter 600 findAllMatches NO
   minTermSize 3 synonyms EXACT ONLY
Protein Ontology (PRO)
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model ANY searchStrategy ANY
filterNumber ANY gaps NONE caseMatch CASE FOLD DIGITS
stopWords PubMed wordOrder ANY stemmer NONE
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize ONE/THREE derivationalVariants NONE orderIndLookup OFF
withSynonyms YES scoreFilter 600 findAllMatches NO
   minTermSize 3/5 synonyms ALL
NCBI Taxonomy
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model ANY searchStrategy SKIP ANY/ALLOW
filterNumber ANY gaps NONE caseMatch ANY
stopWords ANY wordOrder ORDER MATTERS stemmer BioLemmatizer
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords PubMed
minTermSize FIVE derivationalVariants NONE orderIndLookup OFF
withSynonyms ANY scoreFilter 0/600 findAllMatches NO
   minTermSize 3 synonyms EXACT ONLY
ChEBI
NCBO Annotator   MetaMap   ConceptMapper  
Parameter Value Parameter Value Parameter Value
wholeWordOnly YES model STRICT searchStrategy CONTIGUOUS
filterNumber ANY gaps NONE caseMatch ANY
stopWords ANY wordOrder ORDER MATTERS stemmer BioLemmatizer
SWCaseSensitive ANY acronymAbb DEFAULT/UNIQUE stopWords NONE
minTermSize ONE/THREE derivationalVariants NONE orderIndLookup OFF
withSynonyms YES scoreFilter 0/600 findAllMatches YES
   minTermSize 5 synonyms EXACT ONLY
  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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