NERC Environmental Bioinformatics Centre Practical sharing of environmental molecular data Bela Tiwari NERC Environmental Bioinformatics Centre.

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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

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