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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>
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