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 | ||