BioNLP Shared Task 2013 Cancer Genetics task configuration

configurations/BioNLP-ST-2013-CG/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>

configurations/BioNLP-ST-2013-CG/kb_shortcuts.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:
+
+# Keyboard shortcuts for quick type selection in annotation.
+
+G Gene_or_gene_product
+S Simple_chemical
+
+R Regulation
+P	Positive_regulation
+N	Negative_regulation
+E Gene_expression
+A Transcription
+M Metabolism
+
+T Theme
+C Cause