representations

Type Members

1. class Activation extends ComplexEvent

   

   Representation of a Activation.

2. trait AssemblyModification extends AnyRef

   

   Trait for modifications/features associated with an edu.arizona.sista.assembly.representations.Entity.

3. class Complex extends Entity

   

   A Entity representation of a Binding Mention.

4. trait ComplexEvent extends Event

   

   Representation of a ComplexEvent.

5. trait Entity extends EntityEventRepresentation

   

   Trait for entity representations of a Mention.

6. trait EntityEventRepresentation extends Serializable

   

   Trait used for entity/event representations of a Mention.

7. case class EntityLabel(label: String) extends AssemblyModification with Product with Serializable

   

   The label associated with an Entity ( Protein, GGP, etc.)

   The label associated with an Entity ( Protein, GGP, etc.)

   label

   the label associated with an Entity

8. trait Event extends EntityEventRepresentation

   

   Trait for an Event representation of a Mention.

9. case class Location(groundedLoc: GroundingID) extends AssemblyModification with Product with Serializable

   

   A location used in a Translocation

   A location used in a Translocation

   groundedLoc

   the grounding ID associated with an Location

10. case class MutantEntity(mutantType: String) extends AssemblyModification with Product with Serializable

    

    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.

    mutantType

    the type of mutation (see edu.arizona.sista.reach.mentions.Mutant.label)

11. case class PTM(label: String, site: Option[String], negated: Boolean = false) extends AssemblyModification with Product with Serializable

    

    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.

    label

    the ptm

    site

    an Option[String] representing the Site of the PTM

12. class Regulation extends ComplexEvent

    

    Representation of a Regulation.

13. class SimpleEntity extends Entity

    

    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)

14. class SimpleEvent extends Event

    

    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.