D A S for ENCODE data coordination Felix Kokocinski, WTSI

Project Overview Annotate all evidence-based gene features at a high accuracy across the human genome –protein-coding loci with isoforms –nc loci with transcript evidence –pseudogenes Goal: – HAVANA & EnsEMBL, Sanger Institute, UK – University of Lausanne, CH – Centre for Genomic Regulation, ES – Spanish Nat. Cancer Res. Centre, ES – University of California Santa Cruz, USA – Washington University St. Louis, USA – Broad Inst. of MIT and Harvard, USA – Yale University, USA Partners:

Manual Genome Annotation ~20 annotators working according to HAVANA guidelines computational pipeline for alignments Otterlace software input from partner groups, import of data source via DAS verification with RT-PCR, RACE & sequencing

Data Exchange using DAS Distributed Annotation Sources interface WWW GenTrack tracking system Otterlace ann. software high prior. issues exper. ver. issues Perl API Source Adaptors Update Scripts

GenTrack Annotation Tracking extension of open-source RoR ticketing system Redmine ( data import via DAS modules for analyzing and flagging data

GenTrack Annotation Tracking

Entry points: –List of all genes & transcripts in region –High-priority loci –Loci with specific tags Identify problem, compare in Otterlace Resolve by –Changing annotation or –Disbelieving other source –Note decision GenTrack: Workflow

DAS Specifics Format: Specialized 1.53E from sequence ontology (exon: SO: ) (havana_manual_annotation) Evidence code describing the type of method (inferred from RT-PCR experiment (ECO: )) - key=value pairs - parent, lastmod [req] (LASTMOD= T15:15: ) - transcripttype, etc. [opt]

DAS Specifics

Thanks Tim Hubbard ENCODE partners Andy Jenkinson Jonathan Warren Paul Bevan Jody Clements Steve Trevanion James Gilbert Anacode Adam Frankish Toby Hunt Bronwen Aken Steve Searle Jennifer Harrow Redmine.org