# -*- 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 :http://www.uniprot.org/uniprot/?sort=score&query=%s ## GeneOntology :http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?search_query=%s&action=new-search&search_constraint=term ## EntrezGene :http://www.ncbi.nlm.nih.gov/gene?term=%s ## Wikipedia :http://en.wikipedia.org/wiki/%s ## Google :http://www.google.com/search?q=%s ## Alc :http://eow.alc.co.jp/%s Negation box:crossed, glyph:, dashArray: Speculation dashArray:3-3, glyph: Subproc glyph:♲ Nonname glyph:♻