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annotation.conf
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annotation.conf
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# Simple text-based definitions of hierarchial ontologies of
# (physical) entity types, relation types, event types, and
# attributes.
[entities]
Protein
Entity
----------------------------------------
Gene_or_gene_product
Protein_family_or_group
----------------------------------------
Protein_domain_or_region
DNA_domain_or_region
Amino_acid_monomer
----------------------------------------
Carbohydrate
[relations]
Equiv Arg1:Protein, Arg2:Protein
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
Protein-Component Arg1:Gene_or_gene_product|Protein_family_or_group, Arg2:Protein_domain_or_region|DNA_domain_or_region|Amino_acid_monomer
Subunit-Complex Arg1:Gene_or_gene_product, Arg2:Complex
[events]
<GGP-PFG>=Gene_or_gene_product|Protein_family_or_group
<PROTEIN-PART>=Protein_domain_or_region|Amino_acid_monomer
Catalysis|GO:-------|catalysis Theme:<EVENT>, Cause:<GGP-PFG>
----------------------------------------
DNA_methylation|GO:0006306|DNA methylation Theme:Gene_or_gene_product, Site:DNA_domain_or_region
DNA_demethylation|GO:0080111|DNA demethylation Theme:Gene_or_gene_product, Site:DNA_domain_or_region
----------------------------------------
!Protein_modification_process|GO:0006464|protein modification process
Acylation|GO:0043543|protein acylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Acetylation|GO:0006473|protein acetylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Contextgene:Gene_or_gene_product
Palmitoylation|GO:0018345|protein palmitoylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Alkylation|GO:0008213|protein alkylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Methylation|GO:0006479|protein methylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Contextgene:Gene_or_gene_product
Glycosylation|GO:0006486|protein glycosylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Sidechain:carbohydrate
Hydroxylation|GO:0018126|protein hydroxylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Phosphorylation|GO:0006468|protein phosphorylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Lipidation|GO:0006497|protein lipidation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Prenylation|GO:0018342|protein prenylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
# Protein_modification_by_small_protein_conjugation_or_removal|GO:0070647|protein modification by small protein conjugation or removal
!Protein_modification_by_small_protein_conjugation|GO:0032446|protein modification by small protein conjugation
Neddylation|GO:0045116|protein neddylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Sumoylation|GO:0016925|protein sumoylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Ubiquitination|GO:0016567|protein ubiquitination Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Deacylation|GO:0035601|protein deacylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Deacetylation|GO:0006476|protein deacetylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Contextgene:Gene_or_gene_product
Depalmitoylation|GO:0002084|protein depalmitoylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Contextgene:Gene_or_gene_product
Dealkylation|GO:0008214|protein dealkylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Demethylation|GO:0006482|protein demethylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Deglycosylation|GO:0006517|protein deglycosylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>, Sidechain:Carbohydrate
Dehydroxylation|GO:-------|protein dehydroxylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Dephosphorylation|GO:0006470|protein dephosphorylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Delipidation|GO:0051697|protein delipidation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Deprenylation|GO:-------|protein deprenylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
!Protein_modification_by_small_protein_removal|GO:0070646|protein modification by small protein removal
Deneddylation|GO:0000338|protein deneddylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Desumoylation|GO:0016926|protein desumoylation Theme:<GGP-PFG>, Site:<PROTEIN-PART>
Deubiquitination|GO:0016579|protein deubiquitination Theme:<GGP-PFG>, Site:<PROTEIN-PART>
[attributes]
# Definition of entity and event attributes.
# Format in brief: first tab-separated field is attribute name, second
# a set of key-value pairs. The latter must define "Arg:" which
# specifies what the attribute can attach to (typically "<EVENT>").
# If no other keys are defined, the attribute is taken to be a binary
# flag; otherwise other keys are possible attribute values, and their
# values (the keys') are glyphs to show in visualization if the attribute
# has a non-default value. Default is specified by the special key value
# <DEFAULT>, and the special key value <GLYPH-POS> (value either "left"
# or "right") defines where to show the glyph (default "right").
### BioNLP Shared Task ###
Negation Arg:<EVENT>
Speculation Arg:<EVENT>
### Nactem meta-knowledge annotation ###
# "knowledge type"
!KT Arg:<EVENT>, Investigation:Ⓘ, Analysis:Ⓐ, Observation:Ⓞ, Gen-Fact:Ⓕ, Gen-Method:Ⓜ, Gen-Other:Ⓣ
# "certainty level"
!CL Arg:<EVENT>, L1:➊, L2:➋, L3:➌, <GLYPH-POS>:left
# (polarity, corresponds to GENIA / BioNLP ST Negation)
!Polarity Arg:<EVENT>, Negative:✕, Positive:✓, <DEFAULT>:Positive, <GLYPH-POS>:left
!Manner Arg:<EVENT>, High:↑, Low:↓, Neutral:↔, <DEFAULT>:Neutral
!Source Arg:<EVENT>, Other:⇗, Current:⇙, <DEFAULT>:Current