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.
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 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 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.
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 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 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 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 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 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 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 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 to implement an incrementing counter for generating unique IDs.
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 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 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.
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 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 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.
KB MetaInfo is, at minimum, a map of string keys/values.
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.
Factory class for creating and loading a ReverseLookupKB from a TSV file.
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: Repurpose manual KBs to 2nd highest priority.
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: Add flag to allow grounding to ignore species and use human default.
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.
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 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.
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.
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: Replace ChEBI and HMDB KBs with PubChem.
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 tissue type KB.
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: Update for context tissue types KB.
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: Change manual KBs to be ad hoc KBs.
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: Update for use of Uberon as organ KB.
Trait Companion Object allows Mixin OR Import pattern.
Support methods for writing local KB accessors.
Support methods for writing local KB accessors. Written by Tom Hicks. 10/23/2015. Last Modified: Change species selector functions to use sequences.
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.
Trait Companion Object allows Mixin OR Import pattern.
Package object for grounding. Written by: Tom Hicks. 1/15/2016. Last Modified: Redo to return resolution sequences.