Table 2 System parameter description and values
NCBO Annotator parameters | |
|---|---|
Parameter | Description and possible values |
wholeWordOnly | Term recognition must match whole words - (YES, NO) |
filterNumber | Specifies whether the entity recognition step should filter numbers - (YES, NO) |
stopWords | List of stop words to exclude from matching - (PubMed - commonly found terms from PubMed (included as Additional file 1), NONE) |
stopWordsCaseSensitive | Whether stop words are case sensitive - (YES, NO) |
minTermSize | Specifies minimum length of terms to be returned - (ONE, THREE, FIVE) |
withSynonyms | Whether to include synonyms in matching - (YES, NO) |
MetaMap parameters | |
Parameter | Description and possible values |
model | Determines which data model is used - (STRICT - lexical, manual, and syntactic filtering are applied, RELAXED - lexical and manual filtering are used) |
gaps | Specifies how to handle gaps in terms when matching - (ALLOW, NONE) |
wordOrder | Specifies how to handle word order when matching - (ORDER MATTERS, IGNORE) |
acronymAbb | Determines which generated acronym or abbreviations are used - (NONE, DEFAULT, UNIQUE - restricts variants to only those with unique expansions) |
derivationalVars | Specifies which type of derivational variants will be used - (NONE, ALL, ONLY ADJ NOUN) |
scoreFilter | MetaMap reports a score from 0–1000 for every match, with 1000 being the highest, those matches with scores ≤ will be returned - (0, 600, 800, 1000) |
minTermSize | Specifies minimum length of terms to be returned - (ONE, THREE, FIVE) |
ConceptMapper parameters | |
Parameter | Description and possible values |
searchStrategy | Specifies the dictionary lookup strategy - (CONTIGUOUS - longest match of contiguous tokens, SKIP ANY - returns longest match of not-necessarily contiguous tokens and next lookup begin in next span, SKIP ANY ALLOW OVERLAP - returns longest match of not-necessarily contiguous tokens in the span and next lookup begin after next token) |
caseMatch | Specifies the case folding mode to use - (IGNORE - fold everything to lower case, INSENSITIVE - fold only tokens with initial caps to lowercase, SENSITIVE - no folding, FOLD DIGIT - fold only tokens with digits to lower case) |
stemmer | Name of the stemmer to use before matching - (Porter - classic stemmer that removes common morphological and inflectional endings from Engish words, BioLemmatizer - domain specific lemmatization tool for the morphological analysis of biomedical literature presented in Liu et al. [48], NONE) |
orderIndependentLookup | Specifies if ordering of tokens within a span can be ignored - (TRUE, FALSE) |
findAllMatches | Specifies if all matches will be returned - (TRUE, FALSE - only the longest match will be returned) |
stopWords | List of stop words to exclude from matching - (PubMed - commonly found terms from PubMed (included as Additional file 1), NONE) |
synonyms | Specifies which synonyms will be included when creating the dictionary - (EXACT ONLY, ALL) |