annotation.conf
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# -*- 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>