Uses of Package
de.hu.berlin.wbi.objects

Packages that use de.hu.berlin.wbi.objects

Package	Description
cnveth	Package for copy number variation detection of genes (e.g., Aplification of BRCA1) Currently, this package is not used by SETH
de.hu.berlin.wbi.objects	Package with the main data objects.
seth	Package contains most logic of SETH
seth.ner.wrapper	Java wrapper for accessing the scala part of SETH (aka SETH-NER) SETH-NER performs Named Entity Recognition of variation mentions in the latest HGVS nomenclature based on a Backus Naur grammar

Classes in de.hu.berlin.wbi.objects used by cnveth

Class and Description
MutationMention Class to represent a mutation mention found by an NER tool like MutationFinder or SETH

Classes in de.hu.berlin.wbi.objects used by de.hu.berlin.wbi.objects

Class and Description
DatabaseConnection Convenience class for database communication
dbSNP Represents a dbSNP entry; loaded from a local database.
dbSNPNormalized Represents a MutationMention mention which has been successfully normalized to a dbSNP .
EntityOffset Represents the text span of entity mentions (MutationMention, Gene, etc.).
Gene Represents a gene mention found by any Named Enttiy Recognition and Normalization tool.
HGVS Represents a HGVS reference, like NR_027062.1:c.157+25766C>T.
MatchOptions Represents the different possibilities to match a MutationMention to a dbSNP entry or UniProt entry
MutationMention Class to represent a mutation mention found by an NER tool like MutationFinder or SETH
MutationMention.Tool Enumeration of all named entity recognition components
MutationValidation This object represents a MutationMention from the validation corpus, where we already know which dbSNP entry is associated with this gene.
Transcript Class to represents a transcript (Protein as well as coding sequence) Therefore one gene usually contains one or more Transcript
TranscriptNormalized Represents a MutationMention mention which has been successfully normalized to a Transcript .
UniprotFeature Represents a UniProt entry; loaded from database.

Classes in de.hu.berlin.wbi.objects used by seth

Class and Description
MutationMention Class to represent a mutation mention found by an NER tool like MutationFinder or SETH

Classes in de.hu.berlin.wbi.objects used by seth.ner.wrapper

Class and Description
MutationMention Class to represent a mutation mention found by an NER tool like MutationFinder or SETH