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taxonomy.yml.txt
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/
taxonomy.yml.txt
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- 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
- Amount:
- IncreaseAmount:
- Transcription
- DecreaseAmount
- 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