cothec / brat4ref

# -*- 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

Person | Person
Organization | Organization | Org
GPE | Geo-political entity | GPE

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

Be-born | Be born
Transfer-ownership | Transfer ownership
Transfer-money | Transfer money
Start-org | Start org
Merge-org | Merge org
End-org | End org

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

### ACE'05(ish) roles

Agent-Arg | Agent
Artifact-Arg | Artifact
Beneficiary-Arg | Beneficiary
Buyer-Arg | Buyer
Giver-Arg | Giver
Money-Arg | Money
Org-Arg | Org
Person-Arg | Person
Place-Arg | Place
Recipient-Arg | Recipient
Seller-Arg | Seller

[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

Person	bgColor:#ffccaa
Organization	bgColor:#8fb2ff
GPE	bgColor:#7fe2ff
Location	bgColor:#6fffdf
Facility	bgColor:#aaaaee
Vehicle	bgColor:#ccccee
Weapon	bgColor:darkgray
Money	bgColor:#007000, fgColor:white

Alias	dashArray:3-3, arrowHead:none
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>
Confidence      glyph:↑|↔|↓
Speculation	dashArray:3-3, glyph:<NONE>


# Other options

[options]

# Currently, only Arcs bundle is supported here
# Possible values:
# * none: do not bundle arcs
# * all: bundle all arcs
# * space: pack space, but do not bundle arcs
#          (actually, any value other than "none" and "all")
Arcs bundle:none