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:

[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

#Anatomical_entities###

#Organism
Organism_subdivision | Organism subdivision | Org subdiv | Subdiv | SD
Organ_system | Organ system | Ogn sys | OSys | OS
Organ | Organ | Ogn
Multi-tissue_structure | Multi-tissue structure | Multi-tissue | MTissue
Tissue | Tissue
Cell | Cell
Developing_anatomical_structure | Developing anatomical structure | Developing structure | Developing
Subcellular_structure | Subcellular structure | Subcell struct | SubCell | SCell | SC
Pathological_formation | Pathological formation | Pathological form | Path form | PathF | PF
Cancerous_formation | Cancerous formation | Cancer (f)
Cancer | Cancer
Organism_substance | Organism substance | Org subst | OSubst | OSub | OS
Immaterial_anatomical_entity | Immaterial anatomical entity | Immaterial | Imat | IM
Cellular_component | Cellular component | Cell comp

Carcinogenesis | Carcinogenesis | C gen
Cell_transformation | Cell transformation | Cell trans | C trans
Metastasis | Metastasis | Metast

#####
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

### Event types

Protein_catabolism | Protein catabolism | Catabolism | Catab
Gene_expression | Gene expression | Expression | Expr
Binding | Binding | Bind
Transcription | Transcription | Trns
Development   | Development   | Devel | Dv
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
Simple_chemical | Simple chemical | Chemical | Chem
Core_Angiogenesis_Term | Core_Angiogenesis_Term | Core_Angiogenesis | Core_Angio
Other_pharmaceutical_agent | Other_pharmaceutical_agent | Other_pharm
Not_sure | Not_sure | ?
Cell_type | Cell_type | Cell_t | Cell
Planned_process | Planned process | Plan_proc | Pl_prc
Blood_vessel_development | Blood vessel development | BVdev
# end AZ additions

### Relation types

Equiv | Equiv | Eq
Protein-Component | Protein-Component | Component | Comp
Subunit-Complex | Subunit-Complex | Complex | Cmplx

### Role types

Theme  | Theme  | Th
Theme1 | Theme1 | Th1
Theme2 | Theme2 | Th2
Theme3 | Theme3 | Th3
Theme4 | Theme4 | Th4
Cause  | Cause  | Ca
Site   | Site   | Si
Site1  | Site1  | Si1
Site2  | Site2  | Si2
Site3  | Site3  | Si3
Site4  | Site4  | Si4
CSite  | CSite  | CSi 
Contextgene | Contextgene | CGn
Sidechain   | Sidechain   | SCh
Participant | Participant | Pa
Instrument  | Instrument  | Inst | In

patient | patient | ptnt
age | age
gender | gender | gndr
ethnicity | ethnicity | ethn
mutation | mutation | mttn
disease | disease | dis
characteristic | characteristic | char
body-part | body-part | bodp
location | location | loc

[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.
# - 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, dashArray:-

#Protein	bgColor:deepskyblue
#Entity	bgColor:lightskyblue

Equiv	dashArray:3-3, arrowHead:none

# Anatomical entity span colors and related

Pathological_formation	bgColor:#aaaaaa
Cancerous_formation	bgColor:#000000, fgColor:#ffffff
Cancer	bgColor:#000000, fgColor:#ffffff

Organism_subdivision	bgColor:#ddaaaa
Anatomical_system	bgColor:#ee99cc
Organ	bgColor:#ff95ee
Multi-tissue_structure	bgColor:#e999ff
Tissue	bgColor:#cf9fff
Developing_anatomical_structure	bgColor:#ff9fff
Cell	bgColor:#cf9fff
Cellular_component	bgColor:#bbc3ff
Organism_substance	bgColor:#ffeee0
Immaterial_anatomical_entity	bgColor:#fff9f9

REVISE	bgColor:#ff0000,fgColor:#ffffff

# MLEE additions
Blood_vessel_development	bgColor:#ee5a5a
Carcinogenesis	bgColor:#770000, fgColor:#ffaaaa
Cell_transformation	bgColor:#770000, fgColor:#ffaaaa
Metastasis	bgColor:#000077, fgColor:#aaaaff

# BioNLP ST entity and event span colors and related

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
Simple_chemical	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
Cell_type	bgColor:#cf9fff
Organic_compound_other	bgColor:#9fc2ff

gene	bgColor:#7fa2ff
patient	bgColor:#bfafff
body-part	bgColor:#b4c8ff
mutation	bgColor:#7fb6af
characteristic	bgColor:#afd6cf
disease	bgColor:#ef7f7f
location	bgColor:#efefff
gene-or-gene-product	bgColor:#7fa2ff

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
Other	bgColor:#ff0000
Not_sure	bgColor:#ff0000
Other_entity	bgColor:#ff0000
Not_sure_entity	bgColor:#ff0000
Other_event	bgColor:#ff0000
Not_sure_event	bgColor:#ff0000
UNCLASSIFIED	bgColor:#ff0000
Descriptive_reference	bgColor:#aa0000
Planned_process	bgColor:#ff00ff

# BioNLP ST event participant roles

Cause	color:#007700
Cause1	color:#007700
Cause2	color:#007700
Cause3	color:#007700
Cause4	color:#007700
Site	color:#0000aa
Site1	color:#0000aa
Site2	color:#0000aa
Site3	color:#0000aa
Site4	color:#0000aa
CSite	color:#0000aa
ToLoc	color:#0000cc
AtLoc	color:#0000cc
FromLoc	color:#0000cc
Contextgene	color:#303030
Sidechain	color:#303030

atLoc	color:#0000cc
toLoc	color:#0000cc
fromLoc	color:#0000cc

# TODO: check if these are needed, remove if not
#relatedTo	color:#af0000
#scatter	color:#ff0000
#cause	color:#007700

# BioNLP ST relations

Protein-Component	color:#000077

### BEGIN: For Japanese Modality Annotations

# "Entities"
FUTURE	bgColor:#7fa2ff
NON_FUTURE	bgColor:#bfafff
MODAL_PRED	bgColor:#b4c8ff

# "Events"
EPISTEMIC_1_99	bgColor:#7fb6af
FACTIVE	bgColor:#afd6cf
HEARSAY	bgColor:#ef7f7f
OTHER_EPISTEMIC_1_99	bgColor:#efefff
ZERO_MODAL	bgColor:#8fcfff

# "Roles"

# (all default visuals)

### END: For Japanese Modality Annotations

## [search]
## UniProt	<URL>:http://www.uniprot.org/uniprot/?sort=score&query=%s
## GeneOntology    <URL>:http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?search_query=%s&action=new-search&search_constraint=term
## EntrezGene	<URL>:http://www.ncbi.nlm.nih.gov/gene?term=%s
## Wikipedia	<URL>:http://en.wikipedia.org/wiki/%s
## Google	<URL>:http://www.google.com/search?q=%s
## Alc	<URL>:http://eow.alc.co.jp/%s

Negation	box:crossed, glyph:<NONE>, dashArray:<NONE>
Speculation	dashArray:3-3, glyph:<NONE>
Subproc glyph:♲
Nonname glyph:♻