iepy-develop/iepy/webui/brat/configurations/Nactem-metaknowledge/visual.conf

[labels]

### physical entity types

Amino_acid_monomer | Amino acid monomer | AA
Body_region | Body region | Body reg
Carbohydrate | Carbohydrate | Carb
Cell_component | Cell component | Cell comp
Cell_cultured | Cell cultured | Cell
Cell_natural | Cell_natural | Cell
DNA_domain_or_region | DNA domain or region | DDR
DNA_family_or_group | DNA family or group | DFG
DNA_molecule | DNA molecule | DNA
DNA_substructure | DNA substructure | DNA substruct
Element | Element
Inorganic_compound | Inorganic compound | Inorganic
Lipid | Lipid
Multicellular_organism_genetically_modified | Multicellular organism genetically modified | Multicellular organism | Organism
Multicellular_organism_natural | Multicellular organism natural | Multicellular organism | Organism
Nucleotide | Nucleotide
Organic_compound_other | Organic compound other | Organic compound
Peptide | Peptide
Polynucleotide | Polynucleotide
Protein_complex | Protein complex | Complex
Protein_domain_or_region | Protein domain or region | PDR
Protein_family_or_group | Protein family or group | PFM
Protein_molecule | Protein molecule | Prot mol
Protein_substructure | Protein substructure | Protein substruct
RNA_domain_or_region | RNA domain or region | RDR
RNA_family_or_group | RNA family or group | RFG
RNA_molecule | RNA molecule | RNA
RNA_substructure | RNA substructure | RNA substruct
Tissue_cultured | Tissue cultured | Tissue
Tissue_natural | Tissue natural | Tissue
Unicellular_organism | Unicellular organism | Organism
Virus | Virus

### Event types

Artificial_process | Artificial process | Artif proc
Binding | Binding | Bind
Biological_process | Biological process | Bio proc
Cell_adhesion | Cell adhesion | Cell adh
Cell_communication | Cell communication | Cell comm
Cell_differentiation | Cell differentiation | Cell diff
Cell_recognition | Cell recognition | Cell recog
Cellular_physiological_process | Cellular physiological process | Cell phys proc
Cellular_process | Cellular process | Cell proc
Correlation | Correlation
DNA_metabolism | DNA metabolism | DNA metabol
DNA_modification | DNA modification | DNA_mod
DNA_recombination | DNA recombination | DNA recomb
Gene_expression | Gene expression | Expression | Expr
Initiation_of_viral_infection | Initiation of viral infection | Init infect
Localization | Localization | Locl
Metabolism | Metabolism | Metabol
Molecular_Function | Molecular Function | Mol Funct
Mutagenesis | Mutagenesis | Mutagen
Physiological_process | Physiological process | Phys proc
Protein_amino_acid_acetylation | Protein amino acid acetylation | Acetylation | Acet
Protein_amino_acid_deacetylation | Protein amino acid deacetylation | Deacetylation | -Acet
Protein_amino_acid_dephosphorylation | Protein amino acid dephosphorylation | Dephosphorylation | -Phos
Protein_amino_acid_phosphorylation | Protein amino acid phosphorylation | Phosphorylation | Phos
Protein_catabolism | Protein catabolism | Catabolism | Catab
Protein_metabolism | Protein metabolism | Metabolism | Metabol
Protein_modification | Protein modification | Modification | Modif
Protein_processing | Protein processing | Prot proc
Protein_ubiquitination | Protein ubiquitination | Ubiquitination | Ubiq
RNA_metabolism | RNA metabolism | RNA metabol
Transcription | Transcription | Trns
Translation | Translation | Trnslat
Viral_life_cycle | Viral life cycle

Regulation | Regulation | Reg
Positive_regulation | Positive regulation | +Regulation | +Reg
Negative_regulation | Negative regulation | -Regulation | -Reg

### Metaknowledge cues

Polarity-Cue | Polarity-Cue | Pol-Cue
KT-Cue | KT-Cue
CL-Cue | CL-Cue
Manner-Cue | Manner-Cue | Mnr-Cue
Source-Cue | Source-Cue | Src-Cue

### Role types

Theme  | Theme  | Th
Cause  | Cause  | Ca
Cue    | Cue

[drawing]

SPAN_DEFAULT	fgColor:black, bgColor:lightgreen, borderColor:darken
ARC_DEFAULT	color:black, dashArray:-, arrowHead:triangle-5
ATTRIBUTE_DEFAULT	glyph:*

# TODO: clean up, this contains many unnecessary drawing specifications

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

# Metaknowledge cues

Polarity-Cue bgColor:lightgray
KT-Cue bgColor:lightgray
CL-Cue bgColor:lightgray
Manner-Cue bgColor:lightgray
Source-Cue bgColor:lightgray

### Metaknowledge attribute drawing

Polarity	box:crossed|none, glyph:<NONE>
CL	dashArray:3-6|3-3|-, glyph:<NONE>
KT	glyph:Ⓘ|Ⓐ|Ⓞ|Ⓕ|Ⓜ|Ⓣ
Manner	glyph:↑|↓|↔
Source	glyph:⇗|⇙, position:left