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NERC EnvironmentalBioinformatics Centre
Practical sharing of environmental molecular data
Bela Tiwari
NERC Environmental Bioinformatics Centre
NERC EnvironmentalBioinformatics Centre
CEH Oxford
Univ.Manchester
EBI
Univ. Edinburgh
NERC EnvironmentalBioinformatics Centre
A few numbers
• 101,815,678 entries in Genbank (Rel 170 – Feb 15, 2009)
• 158,001,051 entries in EMBL (Rel 99 – Feb 26, 2009)
• 7754276 entries in Uniprot (Rel 14.9 – March 3, 2009)
• 56217 structures in PDB (March 3, 2009)
• 11448 experiments in GEO
• 7723 experiments in ArrayExpress
• 18702298 entries in PubMed (March 9, 2009)
• 1762936 entries in PubMed Central (March 9, 2009)
NERC EnvironmentalBioinformatics Centre
Structured web forms for (simple) sequence submissions
NERC EnvironmentalBioinformatics Centre
Software for general sequence submissions
NERC EnvironmentalBioinformatics Centre
NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
Impacts on data collected in the areas including:– Biodiversity– Climate Change– Energy– Health– Nutrition
A community based ontology for describing the environment of an organism or biological sample
The 'Env' InitiativeRepresenting environmental research in reporting requirements, data models, data exchange format, controlled vocabularies and ontologies.
http://environmentontology.org/
NERC EnvironmentalBioinformatics Centre
http://nebc.nox.ac.uk/envbase
NERC EnvironmentalBioinformatics Centre
http://handlebar.sf.net
NERC EnvironmentalBioinformatics Centre
Bio-Linux
http://www.bio-linux.net
NERC EnvironmentalBioinformatics Centre
http://www.mibbi.org
NERC EnvironmentalBioinformatics Centre
Terminizer
http://terminizer.org
NERC EnvironmentalBioinformatics Centre
http://nebc.nox.ac.uk/envbase
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
Bioinvestigation Index and ISAcreator
http://www.ebi.ac.uk/bioinvindex
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
AcknowledgementsNEBCCEH Oxford
Dawn FieldBela TiwariTim BoothTim BoothJorge SoaresHanny Nuhu
University of ManchesterDave HancockNorman Morrison
EBIChris Taylor
NERCPamela KemptonJason SnapeMark Thorley
University of ManchesterGiles Velarde
EBISusanna SansonePhilippe Rocca-Serra
University of ManchesterMark Blaxter
Many EG and PGP Researchers!
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
• The slides following this one were not in the presentation, but were kept in this file in case questions were asked where they would be useful.
NERC EnvironmentalBioinformatics Centre
MICheckout: Supporting Users
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
TrainingandSupport
Software and Standards Development
BioinformaticsWorkstations NEBC
DataManagement
NERC EnvironmentalBioinformatics Centre
Data volumes have trends like this
NERC EnvironmentalBioinformatics Centre
NERC EnvironmentalBioinformatics Centre
In practice…• Data policy
• Standards
• Software
• Data management
• Support