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

DistributedAnnotationSources

interfaceWWW

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 (www.redmine.org)• data import via DAS• modules for analyzing and flagging data• www.sanger.ac.uk/gentrack

GenTrack Annotation Tracking

GenTrack Annotation Tracking

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GenTrack Annotation Tracking

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• 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

<type-id>

from sequence ontology (exon: SO:0000147)

<method>

(havana_manual_annotation)

<type-category>

Evidence code describing the type of method

(inferred from RT-PCR experiment (ECO:0000109))

<note>

- key=value pairs

- parent, lastmod [req] (LASTMOD=2006-04-07T15:15:58+0100)

- transcripttype, etc. [opt]

DAS Specifics

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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