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# Configuration File for Literature Based Discovery
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# All the options in this file are parsed and used as parameters for
# Literature Based Discovery
# Options keys are in <>'s, and values follow directly after with no space.
# As as example, the line "<rankingMethod>ll" will set the 'rankingMethod'
# parameter with a value of 'll' for literature based discovery
#
# For parameters where no value is needed, just write the name of the
# parameter in '<>' (e.g. '<debug>')
# lines started with a # are skipped and may be used for comments
# The ranking procedure to use for LBD
# valid ranking procedures are:
# allPairs (maxBC) - maximum B to C term value
# averageMinimumWeight (AMW) - average of minimum A to B and B to C values
# linkingTermCount* (LTC) - count of shared linking terms
# frequency* (freq) - sum of A to B co-occurrences of shared B terms
# ltcAssociation (LTA) - association measures that use linking terms as inputs
# ltc_AMW - linking term count with AMW as a tie-breaker
#
# *all procedures require a measure to be specified except LTC and freq
<rankingProcedure>averageMinimumWeight
# The association measure to use as a value in the ranking procedure.
# The string is passed directly to UMLS::Association, so as that gets
# updated, new associatio measures will work automatically.
# At the time of this writing, valid arguments are:
# freq - Frequency
# dice - Dice Coefficient
# left - Fishers exact test - left sided
# right - Fishers exact test - right sided
# twotailed - Fishers twotailed test
# jaccard - Jaccard Coefficient
# ll - Log-likelihood ratio
# tmi - Mutual Information
# odds - Odds Ratio
# pmi - Pointwise Mutual Information
# phi - Phi Coefficient
# chi - Pearson's Chi Squared Test
# ps - Poisson Stirling Measure
# tscore - T-score
<rankingMeasure>ll
# The output path of the results of lbd
<implicitOutputFile>sampleOutput
# a comma seperated list of linking (B) term accept semantic groups, which
# restricts the linking terms to the semantic groups specified. Group names
# come directly from the UMLS.
#<linkingAcceptGroups>CHEM,DISO,GENE,PHYS,ANAT
# similar to linking accept groups, this restricts the acceptable linking (B)
# terms to terms within the semantic types listed
#<linkingAcceptGroups>clnd,chem
# a comma seperated list of target (C) term accept semantic groups, which
# restricts the linking terms to the semantic groups specified. Group names
# come directly from the UMLS.
#<targetAcceptGroups>CHEM,GENE
# similar to target termcept groups, this restricts the acceptable target (C)
# terms to terms within the semantic types listed
#<linkingAcceptGroups>clnd,chem
# Input file path for the explicit co-occurrence matrix used in LBD
<explicitInputFile>sampleExplicitMatrix
# A comma seperated list of starting (A) cuis used in LBD
<startCuis>C0001554,C1961131
# A comma seperated list of target (C) cuis. If specified, system enters closed
# discovery mode
#<targetCuis>