grounding

Type Members

class AdHocIMKBFactory extends Speciated with ReachKBKeyTransforms

Factory class for creating and loading an in-memory KB from a mixed-namespaced TSV file.
Factory class for creating and loading an in-memory KB from a mixed-namespaced TSV file. Written by: Tom Hicks. 1/19/2016. Last Modified: Remove spurious import.
class AzFailsafeKBML extends IMKBMentionLookup

KB accessor implementation which always resolves each mention with a local, fake ID.
KB accessor implementation which always resolves each mention with a local, fake ID. Written by: Tom Hicks. 10/28/2015. Last Modified: Refactor singleton instance here.
class IMKBFamilyLookup extends IMKBLookup

Class implementing alternate key lookups for protein family knowledge bases.
Class implementing alternate key lookups for protein family knowledge bases. Written by Tom Hicks. 11/10/2015. Last Modified: Change to class, add IMKB ctor argument.
class IMKBFamilyMentionLookup extends IMKBMentionLookup

Class implementing alternate key mention lookups for protein family knowledge bases.
Class implementing alternate key mention lookups for protein family knowledge bases. Written by Tom Hicks. 11/15/2015. Last Modified: Fix: call superclass constructor.
class IMKBLookup extends KBLookup with KBAltLookup with ReachKBKeyTransforms

Base class merging logic for local Knowledge Base lookups on top of in-memory KB.
Base class merging logic for local Knowledge Base lookups on top of in-memory KB. Written by Tom Hicks. 10/23/2015. Last Modified: Redo grounding step1 to propagate ambiguity.
class IMKBMentionLookup extends IMKBLookup with KBMentionLookup with KBAltMentionLookup

Class implementing logic for local KB Mention lookups on top of base lookups on top of in-memory KB.
Class implementing logic for local KB Mention lookups on top of base lookups on top of in-memory KB. Written by Tom Hicks. 10/28/2015. Last Modified: Change to class, add IMKB ctor argument.
class IMKBMetaInfo extends KBMetaInfo

Class representing meta-information about an external Knowledge Base.
Class representing meta-information about an external Knowledge Base. Written by: Tom Hicks. 10/25/2015. Last Modified: Minimize default arguments.
class IMKBOrganCellTypeLookup extends IMKBLookup

Class implementing alternate key lookups for cell types which can be inferred from the organ name and specific contextual suffixes.
Class implementing alternate key lookups for cell types which can be inferred from the organ name and specific contextual suffixes. Written by Tom Hicks. 12/20/2015. Last Modified: Change to class, add IMKB ctor argument.
class IMKBOrganCellTypeMentionLookup extends IMKBMentionLookup

Class implementing alternate key mention lookups for cell types which can be inferred from the organ name and specific contextual suffixes.
Class implementing alternate key mention lookups for cell types which can be inferred from the organ name and specific contextual suffixes. Written by Tom Hicks. 12/20/2015. Last Modified: Fix: call superclass constructor.
class IMKBProteinLookup extends IMKBLookup

Class implementing alternate key lookups for protein knowledge bases.
Class implementing alternate key lookups for protein knowledge bases. Written by Tom Hicks. 11/10/2015. Last Modified: Change to class, add IMKB ctor argument.
class IMKBProteinMentionLookup extends IMKBMentionLookup

Class implementing alternate key mentions lookups for protein knowledge bases.
Class implementing alternate key mentions lookups for protein knowledge bases. Written by Tom Hicks. 11/15/2015. Last Modified: Fix: call superclass constructor.
class InMemoryKB extends Speciated with ReachKBKeyTransforms

Class implementing an in-memory knowledge base indexed by key and species.
Class implementing an in-memory knowledge base indexed by key and species. Written by: Tom Hicks. 10/25/2015. Last Modified: Add default sort-by-human for resolutions returned from IMKB.
class IncrementingCounter extends AnyRef

Class to implement an incrementing counter for generating unique IDs.
trait KBAltLookup extends Speciated with KBKeyTransforms

Trait for simple and species-specific string lookup in local knowledge bases using alternate key resolutions.
Trait for simple and species-specific string lookup in local knowledge bases using alternate key resolutions. Written by Tom Hicks. 11/15/2015. Last Modified: Redo to return resolution sequences.
trait KBAltMentionLookup extends KBAltLookup

Trait for simple and species-specific Mention lookup in local knowledge bases using alternate key lookups.
Trait for simple and species-specific Mention lookup in local knowledge bases using alternate key lookups. Written by Tom Hicks. 11/15/2015. Last Modified: Redo to return resolution sequences.
class KBEntry extends Speciated with Serializable

Class holding information about a specific entry from an external Knowledge Base.
Class holding information about a specific entry from an external Knowledge Base. Written by: Tom Hicks. 10/25/2015. Last Modified: Refactor namespace:ID method to utils class.
trait KBKeyTransforms extends AnyRef

Methods for transforming text strings into potential keys for lookup in KBs.
Methods for transforming text strings into potential keys for lookup in KBs. Written by Tom Hicks. 10/22/2015. Last Modified: Update for case-insensitive transforms.
trait KBLookup extends Speciated

Trait for simple and species-specific string lookup in local knowledge bases.
Trait for simple and species-specific string lookup in local knowledge bases. Written by Tom Hicks. 10/28/2015. Last Modified: Redo to return resolution sequences.
trait KBMentionLookup extends KBLookup

Trait for simple and species-specific Mention lookup in local knowledge bases.
Trait for simple and species-specific Mention lookup in local knowledge bases. Written by Tom Hicks. 10/28/2015. Last Modified: Redo to return resolution sequences.
type KBMetaInfo = HashMap[String, String]

KB MetaInfo is, at minimum, a map of string keys/values.
class KBResolution extends Serializable

Class holding information about a specific resolution from the in-memory Knowledge Base.
Class holding information about a specific resolution from the in-memory Knowledge Base. Written by: Tom Hicks. 10/25/2015. Last Modified: Make class serializable.
class RLKBFactory extends AnyRef

Factory class for creating and loading a ReverseLookupKB from a TSV file.
class ReachEntityLookup extends AnyRef

Class which implements project internal methods to ground entities.
Class which implements project internal methods to ground entities. Written by Tom Hicks. 11/9/2015. Last Modified: Restrict to bio mentions. Remove unused state arguments. Fix: bioprocess label.
class ReachGrounder extends Speciated

Class which implements methods to select the best groundings for a sequence of mentions.
Class which implements methods to select the best groundings for a sequence of mentions. Written by Tom Hicks. 2/9/2016. Last Modified: Walk biomentions, match species from context.
trait ReachKBKeyTransforms extends KBKeyTransforms

REACH-related methods for transforming text strings into potential keys for lookup in KBs.
REACH-related methods for transforming text strings into potential keys for lookup in KBs. Written by Tom Hicks. 11/10/2015. Last Modified: Restrict PTM patterns per issue #90.
type Resolutions = Option[Seq[KBResolution]]
class ReverseLookupKB extends AnyRef

Class implementing an in-memory knowledge base indexed by key and species.
Class implementing an in-memory knowledge base indexed by key and species. Written by: Tom Hicks. 3/10/2016 Last Modified: Return immutable sets from lookup.
trait Speciated extends AnyRef

Trait for species features used in external knowledge bases.
Trait for species features used in external knowledge bases. Written by Tom Hicks. 10/23/2015. Last Modified: Add constants and testers for human Namespace:IDs.
class TsvIMKBFactory extends Speciated with ReachKBKeyTransforms

Factory class for creating and loading an in-memory KB from a namespaced TSV file.
Factory class for creating and loading an in-memory KB from a namespaced TSV file. Written by: Tom Hicks. 1/19/2016. Last Modified: Refactor tsv validate fields method to utils class.

Value Members

object AzFailsafeKBML
object EntityChecker extends App

Program to lookup/check incoming BioPax model entities against local knowledge bases.
Program to lookup/check incoming BioPax model entities against local knowledge bases. Author: by Tom Hicks. 5/14/2015. Last Modified: Update for singleton KBL creator.
object KBEntry extends Serializable
def KBMetaInfo: HashMap[String, String]
object ReachContextKBLister

Object implementing logic to enumerate context related KB entries.
Object implementing logic to enumerate context related KB entries. Written by Tom Hicks. 2/19/2016. Last Modified: Add cell component KBs as context KBs.
object ReachEntityLookup
object ReachIMKBLookups

Object which implements all Reach KB Lookup instances.
Object which implements all Reach KB Lookup instances. Written by: Tom Hicks. 10/23/2015. Last Modified: Add family and protein meta info to appropriate KBs.
object ReachIMKBMentionLookups

Object which implements all Reach KB Mention Lookup creators and instances.
Object which implements all Reach KB Mention Lookup creators and instances. Written by: Tom Hicks. 10/28/2015. Last Modified: Refactor singleton instances of KBMLs here.
object ReachKBConstants

Trait for defining constants used by grounding and entity checking code.
Trait for defining constants used by grounding and entity checking code. Written by Tom Hicks. 10/22/2015. Last Modified: Add namespace:ID separator constant.
object ReachKBKeyTransforms extends ReachKBKeyTransforms

Trait Companion Object allows Mixin OR Import pattern.
object ReachKBUtils extends Speciated

Support methods for writing local KB accessors.
Support methods for writing local KB accessors. Written by Tom Hicks. 10/23/2015. Last Modified: Replace nsId selectors with species set selectors.
object ReachRLKBLookups

Object implementing Reach specific reverse lookup tables.
Object implementing Reach specific reverse lookup tables. Written by: Tom Hicks. 3/10/2016 Last Modified: Initial creation.
object Speciated extends Speciated

Trait Companion Object allows Mixin OR Import pattern.

package grounding

Type Members

class AdHocIMKBFactory extends Speciated with ReachKBKeyTransforms

class AzFailsafeKBML extends IMKBMentionLookup

class IMKBFamilyLookup extends IMKBLookup

class IMKBFamilyMentionLookup extends IMKBMentionLookup

class IMKBLookup extends KBLookup with KBAltLookup with ReachKBKeyTransforms

class IMKBMentionLookup extends IMKBLookup with KBMentionLookup with KBAltMentionLookup

class IMKBMetaInfo extends KBMetaInfo

class IMKBOrganCellTypeLookup extends IMKBLookup

class IMKBOrganCellTypeMentionLookup extends IMKBMentionLookup

class IMKBProteinLookup extends IMKBLookup

class IMKBProteinMentionLookup extends IMKBMentionLookup

class InMemoryKB extends Speciated with ReachKBKeyTransforms

class IncrementingCounter extends AnyRef

trait KBAltLookup extends Speciated with KBKeyTransforms

trait KBAltMentionLookup extends KBAltLookup

class KBEntry extends Speciated with Serializable

trait KBKeyTransforms extends AnyRef

trait KBLookup extends Speciated

trait KBMentionLookup extends KBLookup

type KBMetaInfo = HashMap[String, String]

class KBResolution extends Serializable

class RLKBFactory extends AnyRef

class ReachEntityLookup extends AnyRef

class ReachGrounder extends Speciated

trait ReachKBKeyTransforms extends KBKeyTransforms

type Resolutions = Option[Seq[KBResolution]]

class ReverseLookupKB extends AnyRef

trait Speciated extends AnyRef

class TsvIMKBFactory extends Speciated with ReachKBKeyTransforms

Value Members

object AzFailsafeKBML

object EntityChecker extends App

object KBEntry extends Serializable

def KBMetaInfo: HashMap[String, String]

object ReachContextKBLister

object ReachEntityLookup

object ReachIMKBLookups

object ReachIMKBMentionLookups

object ReachKBConstants

object ReachKBKeyTransforms extends ReachKBKeyTransforms

object ReachKBUtils extends Speciated

object ReachRLKBLookups

object Speciated extends Speciated

Inherited from AnyRef

Inherited from Any

Ungrouped