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• taxonomy.yml

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org.clulab.reach.biogrammar.taxonomy.yml Maven / Gradle / Ivy

- Alias
- ModificationTrigger
- Site
- Context:
    - Species
    - CellLine
    - Organ
    - CellType
    - Cellular_component
    - TissueType
    - ContextDirection
    - ContextLocation
    - ContextPossessive
- Modification:
    - PTM
    - Mutant:
        - GenericMutant
        - SubstitutionMutant
        - DeletionMutant
        - DuplicationMutant
        - InsertionMutant
        - FrameshiftMutant
    - EventSite
    - Negation
- PossibleController:
    - Event:
        - SimpleEvent:
            - Binding
            - Generic_event
            - Translocation
            - AdditionEvent:
                - Acetylation
                - Farnesylation
                - Glycosylation
                - Hydrolysis
                - Hydroxylation
                - Methylation
                - Phosphorylation:
                    - AutoPhosphorylation
                - Ribosylation
                - Sumoylation
                - Ubiquitination
            - RemovalEvent:
                - Deacetylation
                - Defarnesylation
                - Deglycosylation
                - Dehydrolysis
                - Dehydroxylation
                - Demethylation
                - Dephosphorylation
                - Deribosylation
                - Desumoylation
                - Deubiquitination
        - ComplexEvent:
            - Regulation:
                - Positive_regulation
                - Negative_regulation
            - ActivationEvent:
                - Positive_activation
                - Negative_activation
    - Entity:
      # Any BioEntity may appear as the controlled in an Activation
      - BioEntity:
          - BioProcess   # ex. "apoptosis"
          - BioChemicalEntity:
              - Generic_entity
              - Simple_chemical
              - Equivalable: #TODO: Better name
                  - Family
                  - MacroMolecule:
                      - Protein
                      - Gene_or_gene_product
                      - Complex
                      - GENE
# a preliminary taxonomy for assembly (precedence relations)
- Precedence:
    # for pairs that are directly (immediately) connected
    # difficult to know from odin rules alone, but not impossible
    - DirectConnection
    # for pairs that are indirectly (not immediately) connected
    - IndirectConnection
    # Between-sentence precedence
    - BetweenSentence:
        - TimexAfter
        - TimexBefore
        - SentenceInitialEvent
        - InterAfter
        - InterBefore
    # tense and aspect detection
    - TAM:
        - Aux
        - Tense:
            - PastTense
            - PresentTense
            - FutureTense
        - Aspect:
            - Perfective
            - Progressive