iepy-develop/iepy/webui/brat/configurations/BioNLP-ST-2013-CG/annotation.conf

# ~/public_html/brat/data/Nactem-AZ/Angiogenesis-1.5.5/

# -*- Mode: Text; tab-width: 2; indent-tabs-mode: nil; coding: utf-8; -*-
# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:

[entities]

# Simple text-based definition of a hierarchial ontology of 
# (physical) entity types.

!Anatomical_entity
 !Material_anatomical_entity
  Organism
  Organism_subdivision
  Anatomical_system
  Organ
  Multi-tissue_structure
  Tissue
  Cell
  Cellular_component
  Organism_substance
  Immaterial_anatomical_entity
  Developing_anatomical_structure
--------------------
Pathological_formation
 Cancer
--------------------
Gene_or_gene_product
Simple_chemical
--------------------
Amino_acid
Protein_domain_or_region
DNA_domain_or_region

[relations]

# Simple text-based definition of a hierarchial ontology of 
# binary relation types.

Equiv	Arg1:Protein_domain_or_region, Arg2:Protein_domain_or_region, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:DNA_domain_or_region, Arg2:DNA_domain_or_region, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Amino_acid, Arg2:Amino_acid, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Gene_or_gene_product, Arg2:Gene_or_gene_product, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Simple_chemical, Arg2:Simple_chemical, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Tissue, Arg2:Tissue, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Organism, Arg2:Organism, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Cell, Arg2:Cell, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Cellular_component, Arg2:Cellular_component, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Pathological_formation, Arg2:Pathological_formation, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Organism_substance, Arg2:Organism_substance, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Anatomical_system, Arg2:Anatomical_system, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Multi-tissue_structure, Arg2:Multi-tissue_structure, <REL-TYPE>:symmetric-transitive
Equiv	Arg1:Cancer, Arg2:Cancer, <REL-TYPE>:symmetric-transitive

# Marks entities that are textually fragmented, as in e.g.
# "alpha- and beta-catenin".

frag	Arg1:Gene_or_gene_product, Arg2:Gene_or_gene_product
frag	Arg1:Protein_domain_or_region, Arg2:Protein_domain_or_region
frag	Arg1:Tissue, Arg2:Tissue
frag	Arg1:Cell, Arg2:Cell
frag	Arg1:Organism, Arg2:Organism
frag	Arg1:Other_pharmaceutical_agent, Arg2:Other_pharmaceutical_agent
frag	Arg1:Simple_chemical, Arg2:Simple_chemical
frag	Arg1:Pathological_formation, Arg2:Pathological_formation
frag	Arg1:Multi-tissue_structure, Arg2:Multi-tissue_structure
frag	Arg1:Organism_subdivision, Arg2:Organism_subdivision
frag	Arg1:Cellular_component, Arg2:Cellular_component
frag	Arg1:Cancer, Arg2:Cancer

# Permitted entity nestings. Defines which entity mention spans in
# text can be contained in which by type. Arg1 identifies the type of
# the inner, Arg2 the type of the outer entity.

ENTITY-NESTING	Arg1:Gene_or_gene_product, Arg2:Organism
ENTITY-NESTING	Arg1:Gene_or_gene_product, Arg2:Tissue
ENTITY-NESTING	Arg1:Gene_or_gene_product, Arg2:Cell
ENTITY-NESTING	Arg1:Gene_or_gene_product, Arg2:Pathological_formation
ENTITY-NESTING	Arg1:Gene_or_gene_product, Arg2:Cancer

[events]

# Simple text-based definition of a hierarchial ontology of event
# types and their arguments.

<MOLECULE>=Gene_or_gene_product|Simple_chemical|Amino_acid
<ANATOMY>=Anatomical_entity|Material_anatomical_entity|Organism_subdivision|Organ_system|Anatomical_system|Organ|Multi-tissue_structure|Tissue|Cell|Cellular_component|Organism_substance|Immaterial_anatomical_entity|Embryonic_structure|Developing_anatomical_structure|Pathological_formation|Cancer

!Protein_or_small_molecule_production_or_breakdown
	Metabolism	Theme:Gene_or_gene_product|Simple_chemical|Amino_acid
		Gene_expression	Theme+:Gene_or_gene_product
			Transcription	Theme:Gene_or_gene_product
			Translation	Theme:Gene_or_gene_product
			Protein_processing	Theme:Gene_or_gene_product
		Synthesis	Theme:Simple_chemical
		Catabolism	Theme:Gene_or_gene_product|Simple_chemical
			Glycolysis	Theme?:Simple_chemical
			Amino_acid_catabolism	Theme?:Simple_chemical
---------
!Cell_or_tissue_production_or_breakdown
	Development	Theme:Organism|<ANATOMY>
		Blood_vessel_development	Theme?:<ANATOMY>, AtLoc?:Organism|<ANATOMY>, ToLoc?:Organism|<ANATOMY>, FromLoc?:Organism|<ANATOMY>
	Growth	Theme:Organism|<ANATOMY>
	Reproduction	Theme:Organism
	Cell_proliferation	Theme:Cell
	Cell_division	Theme:Cell
	Cell_differentiation	Theme?:Cell, AtLoc?:Cancer
	Remodeling	Theme:<ANATOMY>
	Death	Theme:Organism|<ANATOMY>
		Cell_death	Theme?:Cell
	Breakdown	Theme:<ANATOMY>
---------
Mutation	Theme?:Gene_or_gene_product|Cellular_component, Site?:DNA_domain_or_region|Protein_domain_or_region|Amino_acid, AtLoc?:<ANATOMY>
Carcinogenesis	Theme?:Cancer, AtLoc?:<ANATOMY>
 Cell_transformation	Theme?:Cell, AtLoc?:<ANATOMY>
Metastasis	Theme?:Cancer|Cell, ToLoc?:<ANATOMY>
Infection	Theme?:<ANATOMY>|Organism, Participant?:Organism
---------
!Macromolecule_modification
	Phosphorylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Dephosphorylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Methylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Demethylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Glycosylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Deglycosylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Ubiquitination	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Deubiquitination	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Acetylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	Deacetylation	Theme:Gene_or_gene_product|Simple_chemical, Site?:Protein_domain_or_region|Amino_acid
	DNA_methylation	Theme:Gene_or_gene_product|Cellular_component, Site?:DNA_domain_or_region
	DNA_demethylation	Theme:Gene_or_gene_product|Cellular_component, Site?:DNA_domain_or_region
---------
!General_biomolecular_events
	Binding	Theme+:<MOLECULE>|<ANATOMY>, Site?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region
	Dissociation	Theme+:<MOLECULE>|<ANATOMY>
	Localization	Theme+:<MOLECULE>|<ANATOMY>, ToLoc?:<ANATOMY>, AtLoc?:<ANATOMY>, FromLoc?:<ANATOMY>
---------
!Regulation_and_general_causality
	Regulation	Theme:<ENTITY>|<EVENT>, Cause?:<ENTITY>|<EVENT>, Site?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region, CSite?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region
		Positive_regulation	Theme:<ENTITY>|<EVENT>, Cause?:<ENTITY>|<EVENT>, Site?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region, CSite?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region
		Negative_regulation	Theme:<ENTITY>|<EVENT>, Cause?:<ENTITY>|<EVENT>, Site?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region, CSite?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region
---------
!Experimental_intervention
	Planned_process	Theme*:<ENTITY>|Blood_vessel_development, Instrument*:<ENTITY>
--------------------
Pathway	Participant*:<ENTITY>

[attributes]
Negation	Arg:<EVENT>
Speculation	Arg:<EVENT>