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Enzyme reaction annotation guidelines

Entities

entities

  • Amino Acid: Amino acid residues in proteins
  • Cofactor: non-proteins that assist enzyme reactions
  • Functional Group: Parts and atoms that constitute enzymes, amino acids, cofactor and other compounds
  • Enzyme: Enzyme proteins
  • Other Compound: Substances including solvents and non-enzymatic proteins, other than amino acids and cofactors
  • Entity Property: various technical terms

cues

Events

enzyme reaction events

other events

  • Others: A non-enzymatic reaction event
    • Interaction: A non-reaction event; mainly interaction between atoms/functional groups
    • Release: A non-reaction event; dissociation
    • Conformational Change: A non-reaction event; change in conformation/configuration of enzyme/ligand

Relations

  • is_equivalent: Equivalent relation

  • coreference: Co-referent relation; from common expression to more specific/concrete expression (anaphora)

  • cataphora: cataphora, relation similar to coreference, but reference with latter expression

  • corresponds_to: Relation similar to coreference and cataphora, but more specific to reaction-related entities

  • counterpart: counterpart, relation similar to coreference and cataphora but reference with the same entity or event in a different situation

  • group_member: Relation between a countable set and its element; group and member

  • whole_part: Relation between an uncountable set and its subset; whole and part

  • prior_to: Relation for temporal annotation; prior to

  • simultaneous: Relation for temporal annotation; simultaneous

Attributes