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##############################################################################
#            Configuration File for Literature Based Discovery
##############################################################################
# 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

#----- Time Slicing Specific Parameters ------------------------

#Tell LBD to enter precision and recall mode (time slicing)
<precisionAndRecall_implicit>

# name of the file that contains a new line seperated list of cuis
# each cui serves as a start term. The average of all cuis in this
# file are what is reported for precision and recall
<cuiListFileName>timeSliceCuiList

# A list of starting accept types. This is used to randomly generate 100
# starting terms if a cuiListFileName is not specified. All starting terms
# will be of the types listed
<startAcceptTypes>dsyn


#--------------------------------------

# 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

# 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. 
# See https://metamap.nlm.nih.gov/Docs/SemGroups_2013.txt for a list
#<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