Transcript 17-2008-SAB-Tuli

Genetic Data in
Mary Ann Tuli
Growth of Genetic Data
16000
14000
WS120 Mar 2004
12000
WS130 Aug 2004
WS140 Mar 2005
10000
WS150 Nov 2005
8000
WS160 Jul 2006
WS170 Jan 2007
6000
WS180 Sep 2007
4000
WS190 May 2008
2000
0
Approved
Gene Name
Gene Class
Allele
Strain
SAB 2008
Multipoint
data
Growth in Variation Data - 1
12000
10000
8000
Projects
6000
Manual
4000
2000
0
12
WS
0
14
WS
0
160 S 180
S
W
W
SAB 2008
Growth in Variation Data - 2
4000
3500
3000
2500
Lesion
Described
2000
1500
1000
500
0
1
WS
60
1
WS
70
1
WS
80
1
WS
90
• 3500 have rich
annotation
– Description of
lesion
– Connection to
sequence
– Connection to
strain
• In maintenance
SAB 2008
Molecular Change Presentation
SAB 2008
Copy Number Variants
• Generated by Comparative Genome Hybridization
(CGH)
• The University of British of Columbia, Vancouver
Gene Knockout Laboratory
• 249 in WS190
• Displays region which is either definitely or probably
deleted
SAB 2008
Growth in Variation Data - 1
12000
10000
8000
Projects
6000
Manual
4000
2000
0
12
WS
0
14
WS
0
160 S 180
S
W
W
SAB 2008
Large Scale Allele Projects - developments
14000
12000
10000
NRBP
KO Consortium
NemaGENETAG
CNV
8000
6000
4000
2000
0
160
S
W
170
S
W
180
S
W
190
S
W
• Phenotype
192
S
W
information for NRBP alleles sent to CalTech
• NemaGENETAG project data all submitted
• CNV data from KO Consortium
SAB 2008
Genetic Map Data
• We continue to receive data from web
submission forms and publications
• Acedb improvements
• briggsae genetic map - Hillier
SAB 2008
Marey Maps for C. elegans
SAB 2008
Feature Curation
• Will capture
– Binding sites - Consensus sequences - Promoters
• Literature curation (start up)
– Request Tracker (RT) system
• Model changes
• ~60 pending papers
SAB 2008
Other Genomes – Tier II
• Orthologs
– connections stored in Geneace
– names mainly automatically assigned
• Nomenclature guidelines available in Wiki
• Will update WormBook
30000
25000
20000
cloned genes
15000
approved gene names
10000
5000
0
elegans
briggsae
remanei
SAB 2008
Nameservers
• Eases site-to-site collaboration
• Gene Nameserver
– since 2006
– Pre-build checks & scripts
• Variation Nameserver - test version available
• Feature Nameserver
– since 2007
– scripts
SAB 2008
Capturing Data
• From Collaborators
– In-house Web forms – NBP & NemaGENETAG
– E-mail – KO Consortium
• From Users
– WormBase Submission forms
– E-mail – genenames@wormbase
• Within WormBase
– E-mail – Jonathan & First Pass
– Request Tracker (RT) - Feature data
– CalTech forms – Variation
SAB 2008
International Biocurator Society
• Based in Geneva
• ~13 databases
– 3 conference calls
– Wiki
• Sub group formed to compose letter to journals
asking for metadata.
• Next meeting Spring 2009 - Germany
SAB 2008
Future Plans
• Allele curation
– Pre-2001 allele literature
– Richer annotation of existing objects
• Feature literature curation
• Improved capture of data – CalTech
• NemaGENETAG
• Continued website display improvements
SAB 2008
Collaborators
• Nomenclature
– Jonathan Hodgkin
• The CGC
– Ann Rougvie & Theresa Stiernagle
• The Knockout Consortium
– Mark Edgley
– Jeff Holmes
• National BioResource Centre, Japan
– Shohei Mitani
• NemaGENETAG
– Laurent Ségalat
• Acedb
SAB 2008