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h1. {color:#000080}Genomics Import Tool{color}\\

<!--  /* Style Definitions */  table.MsoNormalTable 	{mso-style-name:"Table Normal"; 	mso-tstyle-rowband-size:0; 	mso-tstyle-colband-size:0; 	mso-style-noshow:yes; 	mso-style-priority:99; 	mso-style-parent:""; 	mso-padding-alt:0in 5.4pt 0in 5.4pt; 	mso-para-margin:0in; 	mso-para-margin-bottom:.0001pt; 	mso-pagination:widow-orphan; 	font-size:10.0pt; 	font-family:"Calibri","sans-serif";} --> 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.&nbsp; The development of next generation sequencing  (NGS) has allowed the whole genome to be readily expressed.&nbsp; 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.&nbsp; 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.


h2. 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=1309207298000]*[View Presentation Slides|^genomics-AUG-June-v2.pptx]*&nbsp;from 2013 i2b2 AUG Meeting, Aug 18, 2013, Boston, MA


h2. 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|https://community.i2b2.org/wiki/download/attachments/4554772/Vista+Users+Guide%2C+plugin+and+data.zip?version=1&modificationDate=1323808366000]&nbsp;  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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