# Simple text-based definitions of entity types for the CoNLL 2002 Shared
  # Task on Language-Independent Named Entity Recognition.


[entities]
#Dummy

#MMLite

#Phenotype
Disorder
	Measurement
#	Disease
#	Symptom

Subject
#	N_sbjct
#	Age_sbjct
#	Ethnic_sbjct
#	History_sbjct

Anatomical_entity
#Cell_natural
Cell
	Cell_component
Inorganic_compound
Organic_compound_other
	Pharmacological_substance

GGPs
	#DNA_molecule
	#Protein_molecule
	#Amino_acid_monomer
	#Protein_family_or_grou
	#RNA_molecule

#Value
#	Dose
#	Period
#	Frequency
Entity_Property

#MENTION
Genetic_info

#Artificial_process 
#Biological_process 
#	Binding 
#	Dissociation 

#	Migration 
#	Localization 

#	Regulation 
#		Positive_regulation 
#		Negative_regulation 

#	Cellular_process 
#	Molecular_function 
#		Conversion    
#		Pathway 
#		Gene_expression 
#			#Transcription 
#			#Translation 

###cues
Negation_cue
Speculation_cue
#Manner_cue
Method_cue

[relations] 
#<OVERLAP>	Arg1:<ENTITY>, Arg2:<ENTITY>, <OVL-TYPE>:<ANY>
#ENTITY-NESTING Arg1:Disorder, Arg2:Disorder
#Parameter_Drug	Arg1:Parameter, Arg2:Pharmacological_substance|DRUG|BRAND|GROUP|DRUG_N|GROUP_N|Coreferring_mention
#Parameter_Value		Arg1:Parameter, Arg2:Value

#is_equivalent           Arg1:<ANY>, Arg2:<ANY>
#Coreference		Arg1:<ANY>, Arg2:<ANY>
part_of           Arg1:<ANY>, Arg2:<ANY>
member_of           Arg1:<ANY>, Arg2:<ANY>
Subject_Disorder	Arg1:Subject, Arg2:Disorder
Disorder_association	Arg1:Disorder, Arg2:Disorder

#value_of	Arg1:Value, Arg2:<ANY>
#Subject_Disorder	Arg1:Subject, Arg2:Disease|Symptom


#Coreference		Arg1:Coreferring_mention, Arg2:<ANY>

#is_a			Arg1:<ANY>, Arg2:<ANY>

#Adverse_Effect           Arg1:<ANY>, Arg2:<ANY>
#Interaction           Arg1:<ANY>, Arg2:<ANY>


       	       
[events]

#<GGP-PFG>=Protein_family_or_group|Protein_molecule
<COMPARTMENT>=Cell_component|Cell|Anatomical_entity|Subject|Entity_Property
<MOLECULE>=Organic_compound_other|Pharmacological_substance|Inorganic_compound|GGPs|Amino_acid_monomer|Entity_property
#<MOLECULE>=Organic_compound_other|Pharmacological_substance|Inorganic_compound|DNA_molecule|RNA_molecule|Protein_family_or_group|Protein_molecule|Amino_acid_monomer|Entity_property
#<PROTEIN>=Protein_family_or_group|Protein_molecule|Entity_Property
#<PROTEIN-PART>=Amino_acid_monomer

##<MK-ARGS>=Cue*:Polarity-Cue|KT-Cue|CL-Cue|Manner-Cue|Source-Cue
#<MK-ARGS>=Cue*:Negation_cue|Speculation_cue|Method_cue|Manner_cue
<MK-ARGS>=Cue*:Negation_cue|Speculation_cue|Method_cue

Artificial_process Theme*:<ANY>, Instrument*:<ANY>, disorder*:Disorder, <MK-ARGS>
Biological_process Theme*:<ANY>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, fromLoc?:<COMPARTMENT>, toLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
	Binding Theme*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
	Dissociation Theme*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>

	Localization Theme*:<ANY>, atLoc?:<COMPARTMENT>, fromLoc?:<COMPARTMENT>, toLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>

	Regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>	 
		#Positive_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>	 
		#Negative_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>	 
		Positive_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>	 
		Negative_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>	 

	Correlation Theme*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>	 

	Cellular_process Theme*:<ANY>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
		#Migration 
	Molecular_function Theme*:<MOLECULE>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
		Pathway	   Participant*:<MOLECULE>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
		Conversion Theme*:<MOLECULE>|Cell|Cell_component|Anatomical_entity, Cause:GGPs, Product*:<MOLECULE>, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS>
		Gene_expression	 Theme:GGPs, atLoc?:<COMPARTMENT>, disorder*:Disorder, <MK-ARGS> 
			#Transcription 
			#Translation 

#Artificial_process Theme*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT><MK-ARGS>
#Biological_process Theme*:<ANY>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#	Binding Theme+:<ANY>, Product?:<ANY>, Site*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
## Dissociation (from GPCR corpus)
#	Dissociation Theme?:<MOLECULE>, Product*:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>	
## Migration (Transportation from GPCR corpus)
#	Migration Theme*:<ANY>, FromLoc?:<COMPARTMENT>, ToLoc?:<COMPARTMENT>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#	Localization Theme*:<ANY>, AtLoc?:<COMPARTMENT>, FromLoc?:<COMPARTMENT>, ToLoc?:<COMPARTMENT>, <MK-ARGS>

#	Regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#		Positive_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#		Negative_regulation Theme*:<ANY>, Cause*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>

#	Cellular_process Theme*:<ANY>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#	Molecular_function Theme*:<ANY>, Cause*:<ANY>, Participant*:<ANY>, Product*:<ANY>, atLoc?:<COMPARTMENT>, <MK-ARGS>
## Pathway (from GPCR corpus)
#		Pathway Participant*:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#			Metabolism Participant*:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>
## Biosynthesis, Degradation & Conversion (from GPCR corpus)
#				Biosynthesis  Theme:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#				Degradation   Theme:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#				Conversion    Theme*:<MOLECULE>, Product*:<MOLECULE>, atLoc?:<COMPARTMENT>, <MK-ARGS>

#		Gene_expression Theme:<PROTEIN>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#			Transcription Theme:<PROTEIN>, atLoc?:<COMPARTMENT>, <MK-ARGS>
#			Translation Theme:<PROTEIN>, atLoc?:<COMPARTMENT>, <MK-ARGS>


###Cell_adhesion Theme+:<ANY>, <MK-ARGS>
###Cell_communication Theme*:<ANY>, <MK-ARGS>
###Cell_differentiation Theme*:<ANY>, <MK-ARGS>
###Cell_recognition Theme*:<ANY>, <MK-ARGS>
###Cellular_physiological_process Theme*:<ANY>, <MK-ARGS>

###Correlation Theme*:<ANY>, <MK-ARGS>
###DNA_metabolism Theme*:<ANY>, <MK-ARGS>
###DNA_modification Theme*:<ANY>, <MK-ARGS>
###DNA_recombination Theme*:<ANY>, <MK-ARGS>

###Initiation_of_viral_infection Theme*:<ANY>, <MK-ARGS>

###Mutagenesis Theme*:<ANY>, <MK-ARGS>
###Physiological_process Theme*:<ANY>, <MK-ARGS>
###Protein_amino_acid_acetylation Theme*:<ANY>, <MK-ARGS>
###Protein_amino_acid_deacetylation Theme*:<ANY>, <MK-ARGS>
###Protein_amino_acid_dephosphorylation Theme*:<ANY>, <MK-ARGS>
###Protein_amino_acid_phosphorylation Theme*:<ANY>, <MK-ARGS>
###Protein_catabolism Theme*:<ANY>, <MK-ARGS>
###Protein_metabolism Theme*:<ANY>, <MK-ARGS>
###Protein_modification Theme*:<ANY>, <MK-ARGS>
###Protein_processing Theme*:<ANY>, <MK-ARGS>
###Protein_ubiquitination Theme*:<ANY>, <MK-ARGS>
###RNA_metabolism Theme*:<ANY>, <MK-ARGS>
###Viral_life_cycle Theme*:<ANY>, <MK-ARGS>



#Other_event	has_agent*:<ANY>, theme*:<ANY>, affects*:<ANY>, occurs_at*:<ANY>, has_subject*:Subject, has_cue*:Negation_cue|Speculation_cue|Method_cue	

#PK_mechanism	has_agent*:Pharmacological_substance|DRUG|BRAND|GROUP|DRUG_N|GROUP_N|Combination|Coreferring_mention|DDI, affects*:Parameter|Coreferring_mention, has_subject*:Subject|Coreferring_mention, has_rate*:Value, has_cue*:Negation_cue|Speculation_cue|Manner_cue

[attributes]
#Direction	Arg:<EVENT>, Value:Increase|Decrease|Change
Negated	Arg:<EVENT>
Speculated	Arg:<EVENT>
Certainty	Arg:<EVENT>, Value:Confirmed|Probable|Unlikely
#Manner		Arg:<EVENT>, Value:High|Low|Neutral
Count_sbjct	Arg:Subject, Value:N_sbjct
Gender_sbjct	Arg:Subject, Value:Male|Female|Both
Patient_sbjct	Arg:Subject, Value:Patient|Control
Organism_sbjct	Arg:Subject, Value:Human|Organism