# ~/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, :symmetric-transitive Equiv Arg1:DNA_domain_or_region, Arg2:DNA_domain_or_region, :symmetric-transitive Equiv Arg1:Amino_acid, Arg2:Amino_acid, :symmetric-transitive Equiv Arg1:Gene_or_gene_product, Arg2:Gene_or_gene_product, :symmetric-transitive Equiv Arg1:Simple_chemical, Arg2:Simple_chemical, :symmetric-transitive Equiv Arg1:Tissue, Arg2:Tissue, :symmetric-transitive Equiv Arg1:Organism, Arg2:Organism, :symmetric-transitive Equiv Arg1:Cell, Arg2:Cell, :symmetric-transitive Equiv Arg1:Cellular_component, Arg2:Cellular_component, :symmetric-transitive Equiv Arg1:Pathological_formation, Arg2:Pathological_formation, :symmetric-transitive Equiv Arg1:Organism_substance, Arg2:Organism_substance, :symmetric-transitive Equiv Arg1:Anatomical_system, Arg2:Anatomical_system, :symmetric-transitive Equiv Arg1:Multi-tissue_structure, Arg2:Multi-tissue_structure, :symmetric-transitive Equiv Arg1:Cancer, Arg2:Cancer, :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. =Gene_or_gene_product|Simple_chemical|Amino_acid =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| Blood_vessel_development Theme?:, AtLoc?:Organism|, ToLoc?:Organism|, FromLoc?:Organism| Growth Theme:Organism| Reproduction Theme:Organism Cell_proliferation Theme:Cell Cell_division Theme:Cell Cell_differentiation Theme?:Cell, AtLoc?:Cancer Remodeling Theme: Death Theme:Organism| Cell_death Theme?:Cell Breakdown Theme: --------- Mutation Theme?:Gene_or_gene_product|Cellular_component, Site?:DNA_domain_or_region|Protein_domain_or_region|Amino_acid, AtLoc?: Carcinogenesis Theme?:Cancer, AtLoc?: Cell_transformation Theme?:Cell, AtLoc?: Metastasis Theme?:Cancer|Cell, ToLoc?: Infection Theme?:|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+:|, Site?:Protein_domain_or_region|Amino_acid|DNA_domain_or_region Dissociation Theme+:| Localization Theme+:|, ToLoc?:, AtLoc?:, FromLoc?: --------- !Regulation_and_general_causality Regulation Theme:|, Cause?:|, 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:|, Cause?:|, 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:|, Cause?:|, 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*:|Blood_vessel_development, Instrument*: -------------------- Pathway Participant*: [attributes] Negation Arg: Speculation Arg: