annotation.conf
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# ~/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>