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