# -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:

# Simple text-based definitions of entity, relation and event types
# and event attributes for GENIA PTM annotation.


[entities]

Gene_or_gene_product
Protein_family_or_group
----------------------------------------
Protein_domain_or_region
DNA_domain_or_region
Amino_acid_monomer
----------------------------------------
Carbohydrate


[relations]

Equiv	Arg1:Gene_or_gene_product, Arg2:Gene_or_gene_product
Equiv	Arg1:Protein_family_or_group, Arg2:Protein_family_or_group
Equiv	Arg1:Protein_domain_or_region, Arg2:Protein_domain_or_region
Equiv	Arg1:DNA_domain_or_region, Arg2:DNA_domain_or_region
Equiv	Arg1:Amino_acid_monomer, Arg2:Amino_acid_monomer
Equiv	Arg1:Carbohydrate, Arg2:Carbohydrate


[events]

Catalysis	Theme:<EVENT>, Cause:Gene_or_gene_product|Protein_family_or_group
----------------------------------------
DNA_methylation|GO:0006306	Theme:Gene_or_gene_product, Site:DNA_domain_or_region
DNA_demethylation|GO:0080111	Theme:Gene_or_gene_product, Site:DNA_domain_or_region
----------------------------------------
!Protein_modification_process|GO:0006464
	Acylation|GO:0043543	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Acetylation|GO:0006473	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Contextgene:Gene_or_gene_product
		Palmitoylation|GO:0018345	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Alkylation|GO:0008213	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Methylation|GO:0006479	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Contextgene:Gene_or_gene_product
	Glycosylation|GO:0006486	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Sidechain:Carbohydrate
	Hydroxylation|GO:0018126	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Phosphorylation|GO:0006468	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Lipidation|GO:0006497	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Prenylation|GO:0018342	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
#	Protein_modification_by_small_protein_conjugation_or_removal|GO:0070647
	!Protein_modification_by_small_protein_conjugation|GO:0032446
		Neddylation|GO:0045116	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Sumoylation|GO:0016925	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Ubiquitination|GO:0016567	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Deacylation|GO:0035601	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Deacetylation|GO:0006476	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Contextgene:Gene_or_gene_product
		Depalmitoylation|GO:0002084	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Contextgene:Gene_or_gene_product
	Dealkylation|GO:0008214	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Demethylation|GO:0006482	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Deglycosylation|GO:0006517	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer, Sidechain:Carbohydrate
	Dehydroxylation|GO:-------	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Dephosphorylation|GO:0006470	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	Delipidation|GO:0051697	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Deprenylation|GO:-------	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
	!Protein_modification_by_small_protein_removal|GO:0070646
		Deneddylation|GO:0000338	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Desumoylation|GO:0016926	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer
		Deubiquitination|GO:0016579	Theme:Gene_or_gene_product|Protein_family_or_group, Site:Protein_domain_or_region|Amino_acid_monomer


[attributes]

Negation	Arg:<EVENT>
Speculation	Arg:<EVENT>