Visualizer: Entities and Events

The following are the entities, events, attributes, and relations currently recognized by the Visualizer web application. These object types are pre-configured in the Visualizer javascript for display via the BRAT javascript client.

Key

type	the token, expected in the BRAT standoff, which identifies this object
labels	the abbreviations which can be displayed for instances of this type (which one is used depends on the width of the text span to be displayed)
args	the types and labels of the arguments expected for this type in the BRAT standoff

ENTITIES:

  type: Cellular_component
  labels: [Cellular_component, CellComp, CC]

  type: Simple_chemical
  labels: [Simple_chemical, Chemical, Chem]

  type: Site
  labels: [Site, Si]

  type: Gene_or_gene_product
  labels: [Gene_or_gene_product, Gene_GP, GGP]

  type: Protein
  labels: [Protein, Pro, P]

  type: Complex
  labels: [Protein_Complex, Complex, Cplx]

ENTITY_ATTRIBUTES:

  type: Origin
  args: [ Target, Rulename ]

  type: Negation
  args: none (attribute present or absent)

  type: Speculation
  args: none (attribute present or absent)

RELATIONS:

  type: Equiv
  labels: [Equivalent, Equiv, Eq]

EVENT_TYPES:

Regulations

  type:  Regulation
  labels: [Regulation, Regulat, Reg]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]


  type:  Positive_regulation
  labels: [Positive_regulation, +Regulation, +Reg]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]


  type:  Activation
  labels: [Activation, Activ, +Act]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]


  type:  Negative_regulation
  labels: [Negative_regulation, -Regulation, -Reg]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]


  type:  Inactivation
  labels: [Inactivation, Inactiv, -Act]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]

Gene Expressions

  type:  Gene_expression
  labels: [Gene_expression, Gene_expr, GeneX]
  args:
    type: Theme, labels: [Theme, Th]


  type:  Transcription
  labels: [Transcription, Transcript, Tsc]
  args:
    type: Theme, labels: [Theme, Th]


  type:  Translation
  labels: [Translation, Translate, Tsl]
  args:
    type: Theme, labels: [Theme, Th]

Conversions

  type:  Conversion
  labels: [Conversion, Conver, Conv]
  args:
    type: Theme, labels: [Theme, Th]
    type: Product, labels: [Product, Prod, Pr]


  type:  Phosphorylation
  labels: [Phosphorylation, Phosphor, +Phos]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Dephosphorylation
  labels: [Dephosphorylation, Dephos, -Phos]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Acetylation
  labels: [Acetylation, Acetyl, +Acet]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Deacetylation
  labels: [Deacetylation, Deacetyl, -Acet]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Glycosylation
  labels: [Glycosylation, Glycosyl, +Glycos]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Deglycosylation
  labels: [Deglycosylation, Deglycos, -Glycos]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Hydroxylation
  labels: [Hydroxylation, Hydroxyl, +Hydr]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Dehydroxylation
  labels: [Dehydroxylation, Dehydrox, -Hydr]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Methylation
  labels: [Methylation, Methyl, +Meth]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Demethylation
  labels: [Demethylation, Demethyl, -Meth]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Ubiquitination
  labels: [Ubiquitination, Ubiquit, +Ubiq]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Deubiquitination
  labels: [Deubiquitination, Deubiq, -Ubiq]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  DNA_methylation
  labels: [DNA_methylation, DNA_methyl, +DNAmeth]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  DNA_demethylation
  labels: [DNA_demethylation, DNA_demeth, -DNAmeth]
  args:
    type: Theme, labels: [Theme, Th]
    type: Cause, labels: [Cause, Ca]
    type: Site,  labels: [Site, Si]


  type:  Degradation
  labels: [Degradation, Degrade, Deg]
  args:
    type: Theme, labels: [Theme, Th]


  type:  Binding
  labels: [Binding, Bind]
  args:
    type: Theme, labels: [Theme, Th]
    type: Product, labels: [Product, Prod, Pr]
    type: Site,  labels: [Site, Si]


  type:  Dissociation
  labels: [Dissociation, Dissoc]
  args:
    type: Theme, labels: [Theme, Th]
    type: Product, labels: [Product, Prod, Pr]


  type:  Pathway
  labels: [Pathway, Path]
  args:
    type: Participant, labels: [Participant, Partic, Pa]


  type:  Localization
  labels: [Localization, Local, Loc]
  args:
    type: Theme, labels: [Theme, Th]
    type: AtLoc, labels: [AtLoc, At]
    type: FromLoc, labels: [FromLoc, From]
    type: ToLoc, labels: [ToLoc, To]


  type:  Protein_with_site
  labels: [Protein_with_site, Pro_w_site, PWS]
  args:
    type: Theme, labels: [Theme, Th]
    type: Site,  labels: [Site, Si]


  type:  Transport
  labels: [Transport]
  args:
    type: Theme, labels: [Theme, Th]
    type: FromLoc, labels: [FromLoc, From]
    type: ToLoc, labels: [ToLoc, To]