annotation.conf
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# -*- Mode: Text; tab-width: 2; indent-tabs-mode: nil; coding: utf-8; -*-
# vim:set ft=conf ts=2 sw=2 sts=2 autoindent: noet
# Simple text-based definitions of entity, relation and event types
# and event attributes for the GeneReg corpus.
#
# Note:
#
# In its original form of the GeneReg corpus is not consistent with the
# BioNLP-ST annotation format, as it defines all events without trigger terms:
#
# E1 NegativeRegulationOfGeneExpression: Cause:T120102 Theme:T13186
#
# Such annotations can be rewritten to compliant binary relations of the form
#
# R1 NegativeRegulationOfGeneExpression Cause:T120102 Theme:T13186
#
# by issuing the following commands:
#
# $ cd GeneReg_V_1.0
# $ perl -pi -e 's/^E(\d+[^:]+):/R$1/' *.a2
#
#
# References:
#
# GeneReg corpus: http://www.julielab.de/Resources/Corpora/GeneReg.html
#
[entities]
# *.a1
Gene
# *.a2
Decrease
Entity
GeneExpression
GeneticModification
Increase
TranscriptionOfGene
RegulationOfGeneExpression
PositiveRegulationOfGeneExpression
NegativeRegulationOfGeneExpression
[relations]
RegulationOfGeneExpression Cause:Gene, Theme:Gene
PositiveRegulationOfGeneExpression Cause:Gene, Theme:Gene
NegativeRegulationOfGeneExpression Cause:Gene, Theme:Gene
#Equiv Arg1:Protein, Arg2:Protein
# (No entity nestings permitted for GE. Could be defined using special
# relation type ENTITY-NESTING if necessary.)
[events]
#RegulationOfGeneExpression Theme:<EVENT>|Gene, Cause?:<EVENT>|Gene
#PositiveRegulationOfGeneExpression Theme:<EVENT>|Gene, Cause?:<EVENT>|Gene
#NegativeRegulationOfGeneExpression Theme:<EVENT>|Gene, Cause?:<EVENT>|Gene
[attributes]
#Negation Arg:<EVENT>
#Speculation Arg:<EVENT>