visual.conf
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[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