grounding
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: Add inactive debugging dump.
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: Update for changing IMKB.
Traits and classes used to access information from external knowledge bases.
Traits and classes used to access information from external knowledge bases. Written by Tom Hicks. 3/18/2015. Last Modified: Port to odin branch: adapt for grounding scheme.
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: Add species for NS/ID method.
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: Refactor to use key transforms.
Class holding meta-information for an in-memory knowledge base instance.
Class holding meta-information for an in-memory knowledge base instance. Written by: Tom Hicks. 10/25/2015. Last Modified: Make this class serializable.
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: Replacement of reverse lookups: add species for NS/ID method.
Class to implement an incrementing counter for generating unique IDs.
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: Add no transforms constant. Remove mention handling.
A record class containing key transforms used to configure an in-memory KB upon instantiation.
A record class containing key transforms used to configure an in-memory KB upon instantiation. Written by: Tom Hicks. 1/1/2017. Last Modified: Redo arguments and defaults for updated lookup/transform logic.
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: Refactor for consistent selfless traits and extension vs imports.
A class to create/manipulate Written by: Tom Hicks.
A class to create/manipulate Written by: Tom Hicks. 1/11/2017. Last Modified: Refactor protein kinase lookup set here.
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: Refactor for consistent selfless traits and extension vs imports.
Class to hold common meta data for different types of knowledge bases.
Class to hold common meta data for different types of knowledge bases. Written by Tom Hicks. 12/11/2016. Last Modified: Make this class 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: Remove key field. Compare text canonicalized to lower case.
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: Update for Bioentities KBs.
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: Update for replacement of reverse lookups.
REACH-related methods for transforming mentions and text strings into potential keys for lookup in KBs.
REACH-related methods for transforming mentions and text strings into potential keys for lookup in KBs. Written by Tom Hicks. 11/10/2015. Last Modified: A little smarter gene name affix stripping.
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: Refactor for consistent selfless traits and extension vs imports.
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: Fix: remove redundant load.
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 Bioentities KBs.
This object does NOT implement the selfless-trait pattern because the class is extended.
Companion object to define useful constants and lookup sets.
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: Update for hiding of KB entry class.
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: Revert to using default (canonical) key transforms.
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: Revert to using default (canonical) key transforms.
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: Move no species value and test here.
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: Modify methods to use species name sets.
Trait Companion Object allows Mixin OR Import pattern.
Package object for grounding. Written by: Tom Hicks. 1/15/2016. Last Modified: Update for refactor of KB meta info.