Table 3.
Best performing parameter combinations for CL and GO subsections
| 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 | ||
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”.