Enzyme reaction annotation guidelines

Entities

• General rules for entities

• Amino Acid: Amino acid residues in proteins

• Cofactor: non-proteins that assist enzyme reactions

• Functional Group

• Enzyme

• Other Compound

• Entity Property: entity properties

• Negation Cue: negation words and phrases

• Speculation Cue: speculation words and phrases

• Method Cue

Events

• Whole Reaction

• Nucleophilic Attack

• Protonation

• Deprotonation

• Stabilisation

• Destabilisation

• Activation

• Inactivation

• Modulation

• Electrophilic Attack

• Cleavage

• Bond Formation

• Hybridisation Change

• Coupling Reaction

• Uncoupling Reaction

• Interaction

• Release

• Conformational Change

• Others

Relations

• is_equivalent

• coreference

• corresponds_to

• group_member

• whole_part

Attributes

• Speculation attributes

• Certainty levels