CMoptions-class: Class to set the options to run the EntityFinder

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

CMoptions is a class that represents Conceptmapper configurations. It allows users to set the possible combinations of different parameters for Conceptmapper running.

This method shows the list of options to run the Entity finder

Usage

## S4 method for signature 'CMoptions'
show(object)

Arguments

object

CMoptions instance

Details

The following methods can be applied to CMoptions

show
paramValueIndex
paramValueIndex<-
SearchStrategy
SearchStrategy<-
CaseMatch
CaseMatch<-
Stemmer
Stemmer<-
StopWords
StopWords<-
OrderIndependentLookup
OrderIndependentLookup
FindAllMatches
FindAllMatches<-
SynonymType
SynonymType<-

Value

the list of options

Slots

paramValueIndex

An integer value to index the 576 parameter combinations

SearchStrategy

The matching strategy for finding concepts in the input text

• CONTIGUOUS_MATCHLongets match of contiguous tokens within enclosing span

• SKIP_ANY_MATCHLongest match of not-necessarily contiguous tokens

• SKIP_ANY_MATCH_ALLOW_OVERLAPLongest match of not-necessarily contiguous tokens, overlapping matches are allowed

CaseMatch

• CASE_IGNOREFold everything to lowercase for matching

• CASE_INSENSITIVEFold only tokens with initial caps to lowercase

• CASE_FOLD_DIGITSFold all (and only) tokens with a digit

• CASE_SENSITIVEPerform no case folding

Stemmer

• BIOLEMMATIZER A stemmer specific for biomedical literature

• PORTER A stemmer that removes the commoner morphological and inflexional endings from words in English

• NONE No word stemming

StopWords

• PUBMED A list of stop words obtained analyzing Pubmed papers

• NONE No stop words

OrderIndependentLookup

• ON Ordering within span is ignored (i.e. 'Breast cancer' would equal 'Cancer breast')

• OFF Ordering is taken into consideration

FindAllMatches

• YES All the matches within the span are found

• NO Only the longest match within the span will be returned

SynonymType

• EXACT_ONLY Only exact synonyms are considered

• ALL All synonym types are included

Examples

options <- new('CMoptions')
opt <- CMoptions()
show(opt)

Onassis documentation built on Nov. 8, 2020, 8:18 p.m.