Representation of a Activation.
Trait for modifications/features associated with an edu.arizona.sista.assembly.Entity.
A Entity representation of a Binding Mention.
Representation of a ComplexEvent.
Trait for entity representations of a Mention.
Trait used for entity/event representations of a Mention.
The label associated with an Entity ( Protein, GGP, etc.)
Trait for an Event representation of a Mention.
A representation of a mutated form of an Entity.
A representation of a mutated form of an Entity. Mutation sites, if present, are encoded in mutantType.
the type of mutation (see edu.arizona.sista.reach.mentions.Mutant.label)
A representation of a post-translational modification (PTM) ( Phosphorylation, Ubiquitination, etc.) associated with an Entity.
A representation of a post-translational modification (PTM) ( Phosphorylation, Ubiquitination, etc.) associated with an Entity.
the ptm
an Option[String] representing the Site of the PTM
Stores precedence information for two distinct EntityEventRepresentation
Stores precedence information for two distinct EntityEventRepresentation
EntityEventRepresentation.equivalenceHash identifying the EER that precedes PrecedenceRelation.after
EntityEventRepresentation.equivalenceHash identifying the EER that follows PrecedenceRelation.before
the mentions that serve as evidence for this precedence relation
the name of the Sieve which found this relation
Representation of a Regulation.
Contains all sieves of the signature (mentions: Seq[Mention], manager: AssemblyManager) => AssemblyManager.
A SimpleEntity representation of a Mention of a Protein, GGP, Simple_chemical, etc.
A SimpleEntity representation of a Mention of a Protein, GGP, Simple_chemical, etc. (see the children of "Entity" in the taxonomy)
Representation for any Mention with the label SimpleEvent.
Representation for any Mention with the label SimpleEvent. Note that a Binding is represented using a Complex.
Runnable for producing sieve-based assembly output from a serialized Dataset.
Utilities for running assembly sieves on a Dataset and writing their output.
Constraints used to validate the output of sieves
Runnable for producing sieve-based assembly output from a directory of papers (.csv or .nxml files)
Utilities commonly used by Sieves