Table 7.
Best parameters for optimizing performance for precision or recall
| 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 | ||