Genomic NGS Tool
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Genomics Import Tool\\">Genomics Import Tool

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--> The characterization of a patient, whether for clinical care or clinical research, is destined to become heavily dependent upon knowing an individual's full genome.  The development of next generation sequencing (NGS) has allowed the whole genome to be readily expressed.  This tool enables an i2b2 data loading process that transforms and organizes the products of NGS pipelines into genomic variant observations expressed in the Sequence Ontology.  These observations can then co-exist with many other clinical observations about a patient and allow the formation of complex translational queries.

This project provides scripts to create the requisite Sequence Ontology metadata as well as software to transform NGS products into ready to load i2b2 observations.

Presentations

https://community.i2b2.org/wiki/download/attachments/4554772/Use+of+Genomic+Variants+in+i2b2.pdf?version=1&modificationDate=1309207096000

https://community.i2b2.org/wiki/download/attachments/4554772/AMIA_Spring_2011_1.pdf?version=1&modificationDate=1309207298000View Presentation Slides from 2013 i2b2 AUG Meeting, Aug 18, 2013, Boston, MA

Software

https://community.i2b2.org/wiki/download/attachments/4554772/Vista+Developers+Guide+and+source+1.0.1.zip?version=1&modificationDate=1323807915000

Genomics import package for users  Package containing plugin jar, data files and User's guide for running the Genomics import tool within version 1.7 of the i2b2 workbench.

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