sharing13mar09bt - ESDS

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2 Οκτ 2013 (πριν από 4 χρόνια και 12 μέρες)

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NERC Environmental

Bioinformatics Centre

Practical sharing of
environmental molecular data


Bela Tiwari


NERC Environmental Bioinformatics Centre


NERC Environmental

Bioinformatics Centre

CEH

Oxford

Univ.

Manchester

EBI

Univ.

Edinburgh


NERC Environmental

Bioinformatics 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 Environmental

Bioinformatics Centre

Structured

web forms

for (simple)
sequence
submissions


NERC Environmental

Bioinformatics Centre

Software for
general
sequence

submissions


NERC Environmental

Bioinformatics Centre

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


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics 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' Initiative

Representing environmental research in reporting requirements, data
models, data exchange format, controlled vocabularies and ontologies.


http://environmentontology.org/


NERC Environmental

Bioinformatics Centre

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


NERC Environmental

Bioinformatics Centre


http://handlebar.sf.net


NERC Environmental

Bioinformatics Centre

Bio
-
Linux

http://www.bio
-
linux.net


NERC Environmental

Bioinformatics Centre

http://www.mibbi.org


NERC Environmental

Bioinformatics Centre


Terminizer

http://terminizer.org


NERC Environmental

Bioinformatics Centre

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


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre

Bioinvestigation Index and ISAcreator

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


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre

Acknowledgements

NEBC

CEH Oxford

Dawn Field

Bela Tiwari

Tim Booth

Tim Booth

Jorge
Soares

Hanny

Nuhu


University of Manchester

Dave Hancock

Norman Morrison


EBI

Chris Taylor


NERC

Pamela Kempton

Jason Snape

Mark Thorley


University of Manchester

Giles Velarde


EBI

Susanna Sansone

Philippe Rocca
-
Serra


University of Manchester

Mark Blaxter



Many EG and PGP Researchers!



NERC Environmental

Bioinformatics Centre



NERC Environmental

Bioinformatics 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 Environmental

Bioinformatics Centre

MICheckout: Supporting Users


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre

Training

and

Support

Software and

Standards

Development

Bioinformatics

Workstations

NEBC

Data

Management


NERC Environmental

Bioinformatics Centre


Data volumes have trends like this

0
20000000
40000000
60000000
80000000
100000000
120000000
3
25
40
48
54
57.1
61
65
69
73
77
81
85
89
93
97
101
105
109
113
117
121
125
129
133
137
141
145
149
153
157
161
165
169
Number of entries in Genbank

Number of Entries

NERC Environmental

Bioinformatics Centre


NERC Environmental

Bioinformatics Centre

In practice…


Data policy


Standards


Software


Data management


Support