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visual.conf
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visual.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:
# Note: this visual.conf is a combination of visual configurations for
# a number of tasks that brat has been applied to. These settings are
# here to provide defaults for new installations, and are not intended
# to be used for reference or a starting point for creating new
# visual.conf files. For simple, clean examples, see the visual.conf
# files in subdirectories of configurations/.
[labels]
# Label definitions for display. The labels are separated by pipe
# characters "|".
# The first label must correspond to the form found first in other
# configuration files. As this form must be valid for use in e.g. the
# BioNLP ST standoff format, it must have only ASCII alphanumerics,
# "_" or "-" (i.e. match '^[a-zA-Z0-9_-]$').
# Labels other than the first define forms that are presented to the
# user in the annotation interface, with the first form being the
# preferred full form and the others abbreviations that will be used
# if fuller forms do not fit in the given space. These have no format
# restrictions and can contain e.g. space (this tends to make the
# first and second columns identical for most terms, which do not
# contain space). Surrounding space is ignored.
### Entity types
Protein | Protein | Pro | Pr | P
Entity | Entity | Ent | En | E
Gene_or_gene_product | Gene or gene product | GGP
Protein_family_or_group | Protein family or group | PFM
DNA_domain_or_region | DNA domain or region | DDR
Protein_domain_or_region | Protein domain or region | PDR
Amino_acid_monomer | Amino acid monomer | AA
Protein_molecule | Protein molecule | Prot.mol
Carbohydrate | Carbohydrate | Carb
Multicellular_organism_natural | Multicellular_organism_natural | M-C Organism | MCOrg
Organism | Organism | Org
Chemical | Chemical | Chem
Two-component-system | Two-component-system | 2-comp-sys | 2CS
Regulon-operon | Regulon-operon | Reg/op
Organ | Organ | Ogn
Pathological_formation | Pathological formation | Pathological form | Path form | Path f | PF
Organism_substance | Organism substance | Ogn subst | OSubst | OSub | OS
Subcellular_structure | Subcellular structure | Subcell struct | SubCell | SCell | SC
Multi_tissue_structure | Multi-tissue structure | Multi-t struct | MT struct | MT
Organism_subdivision | Organism subdivision | Org subdiv | OSubdiv |OSD
Blood_vessel_development | BV development | BV devel
### Event types
Protein_catabolism | Protein catabolism | Catabolism | Catab
Gene_expression | Gene expression | Expression | Expr
Binding | Binding | Bind
Transcription | Transcription | Trns
Localization | Localization | Locl
Regulation | Regulation | Reg
Positive_regulation | Positive regulation | +Regulation | +Reg
Negative_regulation | Negative regulation | -Regulation | -Reg
Phosphorylation | Phosphorylation | Phos
Dephosphorylation | Dephosphorylation | -Phos
Acetylation | Acetylation | Acet
Deacetylation | Deacetylation | -Acet
Hydroxylation | Hydroxylation | Hydr
Dehydroxylation | Dehydroxylation | -Hydr
Glycosylation | Glycosylation | Glyc
Deglycosylation | Deglycosylation | -Glyc
Methylation | Methylation | Meth
Demethylation | Demethylation | -Meth
Ubiquitination | Ubiquitination | Ubiq
Deubiquitination | Deubiquitination | -Ubiq
DNA_methylation | DNA methylation | DNA meth
DNA_demethylation | DNA demethylation | DNA -meth
Catalysis | Catalysis | Catal
Biological_process | Biological process | Biol proc
Cellular_physiological_process | Cellular physiological process | Cell phys proc
Acylation | Acylation | Acyl
Deacylation | Deacylation | -Acyl
Alkylation | Alkylation | Alkyl
Dealkylation | Dealkylation | -Alkyl
Palmitoylation | Palmitoylation | Palm
Depalmitoylation | Depalmitoylation | -Palm
Lipidation | Lipidation | Lipid
Delipidation | Delipidation | -Lipid
Prenylation | Prenylation | Prenyl
Deprenylation | Deprenylation | -Prenyl
Neddylation | Neddylation | Nedd
Deneddylation | Deneddylation | -Nedd
Sumoylation | Sumoylation | Sumo
Desumoylation | Desumoylation | -Sumo
# AZ additions
Drug_or_compound | Drug or compound | Drug/comp | D/C
Core_Angiogenesis_Term | Core Angiogenesis Term | Core Angiogenesis | Core Angio
Other_pharmaceutical_agent | Other_pharmaceutical_agent | Other_pharm
Cell_type | Cell_type | Cell_t | Cell
Planned_process | Planned process | Planned
# end AZ additions
# GREC additions
Gene_Expression | Gene Expression | Expression
Gene_Activation | Gene Activation | Activation
Gene_Repression | Gene Repression | Repression
Experimental_Technique | Experimental Technique | Exp Tech
Laboratory_Technique | Laboratory Technique | Lab Tech
Null_Mutation | Null Mutation
Point_Mutation | Point Mutation
# end GREC additions
### Relation types
Equiv | Equiv | Eq
Protein-Component | Protein-Component | Component | Comp
Subunit-Complex | Subunit-Complex | Complex | Cmplx
### Role types
Theme | Theme | Th
Cause | Cause | Ca
Site | Site | Si
Contextgene | Contextgene | CGn
Sidechain | Sidechain | SCh
Participant | Participant | Pa
Instrument | Instrument | Instr | In
[drawing]
# Other aspects of visual presentation. The format is label (form used
# in other configurations, first of the labels) of the annotation
# separated by tab from comma-separated key:value pairs. The recognized
# keys, their values and purpose are:
# - fgColor : any HTML color specification (e.g. "black"), sets
# the color of a span text in the visualization.
# - bgColor : any HTML color specification (e.g. "white"), sets
# the color of a span "box" background in the visualization.
# - borderColor : any HTML color specification (e.g. "black"), sets
# the color of a span "box" border in the visualization.
# Also supports special value "darken", which specifies to
# use a darker shade of bgColor for the border.
# - color : any HTML color specification (e.g. "black"), sets
# the color of an arc in the visualization.
# - dashArray : any valid SVG stroke-dasharray specification using
# dashes (instead of commas or space) as separators
# (e.g. "3-3"), sets the dash/dot pattern for lines
# in the span/arc visualization ("-" works for solid
# line)
# The special labels "SPAN_DEFAULT" and "ARC_DEFAULT" are recognized
# as setting defaults that will be used for types without specific
# settings. It is not necessary to define all aspects of the
# visualization (e.g. just Color can be given): defaults will be
# used for unspecified cases.
SPAN_DEFAULT fgColor:black, bgColor:lightgreen, borderColor:darken
ARC_DEFAULT color:black, arrowHead:triangle-5
#Protein bgColor:deepskyblue
#Entity bgColor:lightskyblue
Equiv dashArray:3-3, arrowHead:none
# BioNLP ST entity and event span colors and related
Exp bgColor:#cccccc
Sub-Process bgColor:#ee7a7a
Protein bgColor:#7fa2ff
Protein_family_or_group bgColor:#7fa2ff
Protein_complex bgColor:#7fa2ff
Protein_molecule bgColor:#7fa2ff
RNA_molecule bgColor:#7fa2ff
DNA_molecule bgColor:#7fa2ff
DNA_family_or_group bgColor:#7fa2ff
Chemical bgColor:#8fcfff
Carbohydrate bgColor:#8fcfff
Drug_or_compound bgColor:#8fcfff
Other_pharmaceutical_agent bgColor:#8fcfff
Gene_or_gene_product bgColor:#7fa2ff
Lipid bgColor:#9fc2ff
Cell_natural bgColor:#cf9fff
Cell_cultured bgColor:#cf9fff
Virus bgColor:#cf9fff
Organism bgColor:#ffccaa
Tissue bgColor:#cf9fff
Cell_type bgColor:#cf9fff
Organic_compound_other bgColor:#9fc2ff
Positive_regulation bgColor:#e0ff00
Catalysis bgColor:#e0ff00
Regulation bgColor:#ffff00
Negative_regulation bgColor:#ffe000
Deacetylation bgColor:#18c59a
Deglycosylation bgColor:#18c59a
Dehydroxylation bgColor:#18c59a
Demethylation bgColor:#18c59a
Dephosphorylation bgColor:#18c59a
Deubiquitination bgColor:#18c59a
DNA_demethylation bgColor:#18c59a
Deacylation bgColor:#18c59a
Dealkylation bgColor:#18c59a
Depalmitoylation bgColor:#18c59a
Delipidation bgColor:#18c59a
Deprenylation bgColor:#18c59a
Deneddylation bgColor:#18c59a
Desumoylation bgColor:#18c59a
Process bgColor:#9fe67f
Entity bgColor:#b4c8ff
DNA_domain_or_region bgColor:#b4c8ff
Protein_domain_or_region bgColor:#b4c8ff
Amino_acid_monomer bgColor:#b4c8ff
Polynucleotide bgColor:#b4c8ff
Two-component-system bgColor:#9999ff
Regulon-operon bgColor:#9999ff
Experimental_method bgColor:#ffff00
Pathological_formation bgColor:#aaaaaa
Subcellular_structure bgColor:#bbc3ff
Organ bgColor:#e999ff
Multi_tissue_structure bgColor:#e595ff
Organism_substance bgColor:#ffeee0
# Some GREC types (incomplete)
Gene bgColor:#7fa2ff
# BioNLP ST event participant roles
Cause color:#007700
Site color:#0000aa
CSite color:#0000aa
ToLoc color:#0000cc
AtLoc color:#0000cc
Contextgene color:#303030
Sidechain color:#303030
# BioNLP ST relations
Protein-Component color:#000077
# Attributes
ATTRIBUTE_DEFAULT glyph:*
Negation box:crossed, glyph:<NONE>, dashArray:<NONE>
Speculation dashArray:3-3, glyph:<NONE>