annotation.conf
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# Annotation configuration for BioNLP Shared Task 2013
# Pathway Curation (PC) task
[entities]
Simple_chemical
Gene_or_gene_product
Complex
Cellular_component
[relations]
Equiv Arg1:Simple_chemical, Arg2:Simple_chemical, <REL-TYPE>:symmetric-transitive
Equiv Arg1:Gene_or_gene_product, Arg2:Gene_or_gene_product, <REL-TYPE>:symmetric-transitive
Equiv Arg1:Complex, Arg2:Complex, <REL-TYPE>:symmetric-transitive
Equiv Arg1:Cellular_component, Arg2:Cellular_component, <REL-TYPE>:symmetric-transitive
[events]
<MOLECULE>=Simple_chemical|Gene_or_gene_product|Complex
<COMPARTMENT>=Cellular_component
Conversion Theme*:<MOLECULE>, Product*:<MOLECULE>
Phosphorylation Theme:<MOLECULE>, Site?:Simple_chemical
Dephosphorylation Theme:<MOLECULE>, Site?:Simple_chemical
Acetylation Theme:<MOLECULE>, Site?:Simple_chemical
Deacetylation Theme:<MOLECULE>, Site?:Simple_chemical
Glycosylation Theme:<MOLECULE>, Site?:Simple_chemical
Deglycosylation Theme:<MOLECULE>, Site?:Simple_chemical
Hydroxylation Theme:<MOLECULE>, Site?:Simple_chemical
Dehydroxylation Theme:<MOLECULE>, Site?:Simple_chemical
Localization Theme:<MOLECULE>, AtLoc?:<COMPARTMENT>, FromLoc?:<COMPARTMENT>, ToLoc?:<COMPARTMENT>
Transport Theme:<MOLECULE>, FromLoc?:<COMPARTMENT>, ToLoc?:<COMPARTMENT>
Gene_expression Theme:Gene_or_gene_product
Transcription Theme:Gene_or_gene_product
Translation Theme:Gene_or_gene_product
Degradation Theme:<MOLECULE>
Binding Theme+:<MOLECULE>, Product?:Complex, Site*:Simple_chemical
Dissociation Theme?:Complex, Product*:<MOLECULE>
-----
Regulation Theme:<ANY>, Cause?:<ANY>
Positive_regulation Theme:<ANY>, Cause?:<ANY>
Activation Theme:<MOLECULE>, Cause?:<ANY>
Negative_regulation Theme:<ANY>, Cause?:<ANY>
Inactivation Theme:<MOLECULE>, Cause?:<ANY>
-----
Pathway Participant*:<MOLECULE>
[attributes]
Negation Arg:<EVENT>
Speculation Arg:<EVENT>