Changes between Version 16 and Version 17 of i2b2 AUG 2013

Timestamp:

06/24/13 13:34:40 (11 years ago)

Author:

Richard Bramley

Comment:

--

i2b2 AUG 2013

@@ -169 +169 @@
 
 === [=#AUG1 Genomic Cell] ===
+
+Presentation of the new Genome Cell for i2b2 which uses the following pipeline:
+
+1. VCF - variant cell format (variations from a reference genome)
+1. [[http://www.openbioinformatics.org/annovar/|Annovar]]
+1. GVF - Genome Variation Format
+1. i2b2
+ * Observation (snp - no data)
+ * use modifiers to record the snp information
+
+Uses the NCBO genome onthologies.
+
+One problem with recording VCF information is that annotations will change over time.  This is because:
+
+* The reference human genome changes regularly (~once per year).
+* New knowledge changes the way the changes way genomes are annotated (could be much more frequent).
+
 === [=#AUG2 SMART Apps] ===
+
+Presentation of SMART plugin framework for i2b2.
+
+SMART is an API that allows SMART apps 
 === [=#AUG3 i2b2 Roadmap] ===
 === [=#AUG4 Planning for the future] ===
@@ -179 +200 @@
 
 === [=#SHRINE1 SHRINE Clinical Trials (CT) Functionality and Roadmap] ===
-=== [=#SHRINE1 SHRINE National Pilot Lessons Learned] ===
-=== [=#SHRINE1 SHRINE Ontology Panel] ===
-=== [=#SHRINE1 University of California Research Exchange (UC ReX)] ===
-=== [=#SHRINE1 Preparation for Patient-Centred Research] ===
-=== [=#SHRINE1 Case Study: Improve Care Now] ===
+=== [=#SHRINE2 SHRINE National Pilot Lessons Learned] ===
+=== [=#SHRINE3 SHRINE Ontology Panel] ===
+=== [=#SHRINE4 University of California Research Exchange (UC ReX)] ===
+=== [=#SHRINE5 Preparation for Patient-Centred Research] ===
+=== [=#SHRINE6 Case Study: Improve Care Now] ===