Create brat visualization

[MrTimothy20]

-- 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_moleculebgColor:#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_otherbgColor:#9fc2ff
Positive_regulation bgColor:#e0ff00
CatalysisbgColor:#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:#77

Attributes

ATTRIBUTE_DEFAULT glyph:*
Negation box:crossed, glyph:, dashArray:
Confidence glyph:鈫憒鈫攟鈫�
Speculation dashArray:3-3, glyph:

Other options

[options]

Possible values:

* none: do not bundle arcs

* hide: hide intermediate (border-to-border) arc parts

* all: bundle all arcs

* space: pack space (do not try to line up arc height in different lines),

but do not bundle arcs

(actually, any value other than "none", "hide" and "all")

Arcs bundle:none

Possible values:

* rtl: right-to-left script (e.g. Arabic, Hebrew)

* ltr: left-to-right script (e.g. English, Japanese)

(actually, any value other than "rtl")

Text direction:ltr
Workout and Solution
This is a visual.cof file structure combining it with the minimal example configuration in relation to entity,relation
,event type and attribute as specified. Disconfiguration provide the visual presentation setup from the specific
entity of the four types that is relations ,entity types, events and attributes.
-- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; --

vim:set ft=conf ts=2 sw=2 sts=2 autoindent:

[labels]

Entity types

Method | Method
Material | Material
Operate | Operate
Function | Function
Features_Performance_Advantages | Features, Performance, Advantages
Scientific_Concept | Scientific Concept | Sci Concept
Energy | Energy
Substance | Substance
Information | Information
Way | Way
Question | Question
Application_Scenarios | Application Scenarios
Interaction | Interaction
Task | Task
Attributes | Attributes
State | State

Relation types

Located_At | Located at
Adjacent_To | Adjacent to
Part_Of | Part of
Causes | Causes
Leads_To | Leads to
Prevents | Prevents
Before | Before
After | After
Simultaneous | Simultaneous
Used_For | Used for
Dependent_On | Dependent on
Has_Attribute | Has attribute
Characterized_By | Characterized by

Event types

Implementation | Implementation
Execution | Execution
Application | Application
Creation | Creation
Modification | Modification
Combination | Combination
Operation | Operation
Performance | Performance
Failure | Failure
Occurrence | Occurrence
Detection | Detection
Identification | Identification

Attributes

Size | Size
Shape | Shape
Color | Color
Material | Material
Efficiency | Efficiency
Speed | Speed
Accuracy | Accuracy
Status | Status
Condition | Condition
State | State
Value | Value
Quantity | Quantity
Level | Level
[drawing]
SPAN_DEFAULT fgColor:black, bgColor:lightgreen, borderColor:darken
ARC_DEFAULT color:black, arrowHead:triangle-5
Method bgColor:#ffccaa
Material bgColor:#8fb2ff
Operate bgColor:#7fe2ff
FunctionbgColor:#6fffdf
Features_Performance_Advantages bgColor:#aaaaee
Scientific_Concept bgColor:#ccccee
Energy bgColor:darkgray
Substance bgColor:#007000, fgColor:white
Information bgColor:#ffccaa
Way bgColor:#8fb2ff
Question bgColor:#7fe2ff
Application_Scenarios bgColor:#6fffdf
Interaction bgColor:#aaaaee
Task bgColor:#ccccee
Attributes bgColor:darkgray
State bgColor:#007000, fgColor:white
Located_At color:#77
Adjacent_To color:#77
Part_Of color:#77
Causes color:#007700
Leads_To color:#007700
Preventscolor:#007700
Before color:#0000aa
After color:#0000aa
Simultaneous color:#0000aa
Used_For color:#303030
Dependent_On color:#303030
Has_Attribute color:#303030
Characterized_By color:#303030
Implementation bgColor:#e0ff00
Execution bgColor:#e0ff00
Application bgColor:#ffff00
Creation bgColor:#ffe000
Modification bgColor:#18c59a
Combination bgColor:#18c59a
Operation bgColor:#18c59a
Performance bgColor:#18c59a
Failure bgColor:#18c59a
Occurrence bgColor:#18c59a
Detection bgColor:#9fe67f
Identification bgColor:#9fe67f
Size bgColor:#b4c8ff
Shape bgColor:#b4c8ff
Color bgColor:#b4c8ff
Material bgColor:#b4c8ff
Efficiency bgColor:#b4c8ff
Speed bgColor:#b4c8ff
Accuracy bgColor:#b4c8ff
Status bgColor:#b4c8ff
Condition bgColor:#b4c8ff
State bgColor:#b4c8ff
Value bgColor:#b4c8ff
QuantitybgColor:#b4c8ff
Level bgColor:#b4c8ff
[options]
Arcs bundle:none
Text direction:ltr