SETH documentation

Packages

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.
de.hu.berlin.wbi.process	Various common work-flows based on SNP normalization.
de.hu.berlin.wbi.process.osiris	Package to evaluate performance of SETH on the osiris dataset
de.hu.berlin.wbi.stuff.xml	This package is relevant to rebuild the MySQL-Database for SNP normalization purposes
edu.uchsc.ccp.nlp.ei.mutation	Contains the modified MutationFinder code Adaptations include the recognition of ambiguous mutations, non-synonymous mutations, and DNA mutations For the original code we refer to http://mutationfinder.sourceforge.net/
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
seth.seth.eval	Code for applying and evaluating SETH on various corpora