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

NERC EnvironmentalBioinformatics Centre

Practical sharing of environmental molecular data

Bela Tiwari

NERC Environmental Bioinformatics Centre


CEH Oxford

Univ.Manchester

EBI

Univ. Edinburgh


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)


Structured web forms for (simple) sequence submissions


Software for general sequence submissions


NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk




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/


http://nebc.nox.ac.uk/envbase


http://handlebar.sf.net


Bio-Linux

http://www.bio-linux.net


http://www.mibbi.org


Terminizer

http://terminizer.org


http://nebc.nox.ac.uk/envbase



Bioinvestigation Index and ISAcreator

http://www.ebi.ac.uk/bioinvindex





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!



• 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.


MICheckout: Supporting Users




TrainingandSupport

Software and Standards Development

BioinformaticsWorkstations NEBC

DataManagement


Data volumes have trends like this



In practice…• Data policy

• Standards

• Software

• Data management

• Support

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

Documents

environmental research

ukenvbase slide

edinburgh slide

isacreator http

data models

manchester ebi

data exchange format

support software