Table 7 Best parameters for optimizing performance for precision or recall
High precision annotations | |||||
|---|---|---|---|---|---|
NCBO Annotator | Â | MetaMap | Â | ConceptMapper | Â |
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 |
| Â | Â | minTermSize | 3/5 | synonyms | EXACT ONLY |
High recall annotations | |||||
NCBO Annotator | Â | MetaMap | Â | ConceptMapper | Â |
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 |
| Â | Â | minTermSize | 1/3 | synonyms | ALL |