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

Slides:

Advertisements

Similar presentations

I. Spasić,1 D. Schober,2 S. Sansone,2 D. Rebholz-Schuhmann,2 D

Advertisements

HERODOT CONFERENCE: CELEBRATING GEOGRAPHICAL DIVERSITY May 2009, Ayvalik, Turkey.

OpenBiblio: an easy-to-use free Integrated Library System software

Angela McCutcheon, Director of ETD Graduate College Ohio University May 26, 2009.

Martin John Bishop UK HGMP Resource Centre Hinxton Cambridge CB10 1 SB

SUSTAINABILITY IMPACT ASSESSMENT OF THE WTO DOHA AGENDA Clive George Impact Assessment Research Centre Institute for Development Policy and Management.

Update for CDNL Milan 26 August 2009 Caroline Brazier, Chair of ICADS IFLA-CDNL Alliance for Digital Strategies.

Genome Annotation: A Protein-centric Perspective.

Data management, data sharing and the activities of the UKDA Managing research data well workshop London, 30 June 2009 Manchester, 1 July 2009.

Smart Qualitative Data: Methods and Community Tools for Data Mark-Up SQUAD Libby Bishop Online Qualitative Data Resources: Best Practice in Metadata Creation.

The ArrayExpress Gene Expression Database: a Software Engineering and Implementation Perspective Ugis Sarkans European Bioinformatics Institute.

OMII-UK Steven Newhouse, Director. © 2 OMII-UK aims to provide software and support to enable a sustained future for the UK e-Science community and its.

E-Science Update Steve Gough, ITS 19 Feb e-Science large scale science increasingly carried out through distributed global collaborations enabled.

© University of Reading IT Services e-Research workshop Mike Roch, Director of IT Services 17 June 2009.

The MGED Ontology: Providing Descriptors for Microarray Data Trish Whetzel Department of Genetics Center for Bioinformatics University of Pennsylvania.

A centre of expertise in digital information management UKOLN is supported by: Changing Roles, Responsibilities and Relationships Dr Liz.

A centre of expertise in digital information management UKOLN is supported by: Research Data & Institutions Roles & Responsibilities? Dr.

CCPN project modeling framework University of Cambridge European Bioinformatics Institute MSD group.

The Discovery Landscape in Crystallography UKOLN is supported by: Monica Duke UKOLN, University of Bath, UK – eBank UK project A centre.

EBI is an Outstation of the European Molecular Biology Laboratory. DAS implementations Bernat Gel 01/03/11.

Expanding the Reach of Bioinformatics Training Jennifer McDowall, Ph.D. Senior Scientist.

The Institute for Learning and Research Technology is a national centre of excellence in the development and use of technology-based methods in teaching,

Environmental Information Data Centre: enabling the discovery of CEH-held data John Watkins Deputy Director EIDC.

Rule Extraction from trained Neural Networks Brian Hudson, Centre for Molecular Design, University of Portsmouth.

Rafael C Jimenez DAS DAS Workshop 2012 February 27-29, 2012 Using DAS software, an introduction to some DAS implementations.

Databanks (A) NCBINCBI (National Center for Biotechnology Information) is a home for many public biological databases (see an older diagram below). All.

European Bioinformatic Institute.

On the launch of UK PubMed Central Frontiers in Information Management for the Bio- and environmental Sciences Novartis Foundation, 25 Jan 07 Adam Bostanci.

Visualisationmodule Catherine Leroy, Pierre Marguerite, Bhuwan Tiwari, Niran Abeygunawardena, Sergio Contrino, Anna Farne, Ele Holloway, Gaurab Mukherjee,

HCS806 “Methods in Horticulture and Crop Science” Introduction to methods in Bioinformatics for plant science. David Francis (Coordinator) Ian Holford.

Basic Genomic Characteristic  AIM: to collect as much general information as possible about your gene: Nucleotide sequence Databases ○ NCBI GenBank ○

Welcome to mini-symposium on ontologies for biological sample description EMBL-EBI Wellcome Trust Genome Campus Deceber 5, 2001.

Functional Genomics Ontology FuGO and Metabolomics Society Ontology group Susanna-Assunta Sansone Nutr/Toxicogenomics Projects Coordinator EMBL-EBI Metabolomics.

Bioinformatics for biomedicine Summary and conclusions. Further analysis of a favorite gene Lecture 8, Per Kraulis

 Goals Unambiguous description of how the investigation was performed Consistent annotation, powerful queries and data integration  Details NOT model.

Introduction to Web services MSc on Bioinformatics for Health Sciences May 2006 Arnaud Kerhornou Iván Párraga García INB.

1 Enriching UK PubMed Central SPIDER launch meeting, Wolfson College, Oxford Paul Davey, UK PubMed Central Engagement Manager.

Protein databases Morten Nielsen. Background- Nucleotide databases GenBank, National Center for Biotechnology Information.

Data, data standards and sharing Dr Daniel Swan Bioinformatics Support Unit

Bioinformatics.

Databases in Bioinformatics and Systems Biology Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.

VectorBase A Resource Centre for Invertebrate Hosts of Human Pathogens Bob MacCallum Imperial College London.

1 st (RSBI) ISA-Tab Workshop – Scope and Outcome  Tackle today's need for exchange of multi-omics experiments Evaluate the ISA-TAB straw-man (incomplete)

The Web Services Game. This game is intended for a non technical audience; We have purposely simplified technical aspect. 2.

The European Bioinformatics Institute MGED ontology for consistent annotation of microarray experiments Manchester Bioinformatics Week Ontologies Workshop1.

STONY BROOK UNIVERSITY HEALTH SCIENCES LIBRARY CHECK OUT THE SERVICES & RESOURCES AVAILABLE TO YOU.

1 MIAME The MIAME website: © 2002 Norman Morrison for Manchester Bioinformatics.

ArrayExpress – a public database for microarray gene expression data Helen Parkinson Microarray Informatics Team European Bioinformatics Institute MGED.

Wheat Data Interoperability. 2  Endorsed in March 2014  Focus:  Improve/reach semantic interoperability of Wheat data  The WG will focus first on.

The Environmental Genomics Thematic Programme Data Centre Dawn Field, Director.

Gerry Lawson & Pamela Kempton NERC Swindon 21 Sept Development of NERC’s next science strategy: an update for the SEERAD Strategic Science Advisory.

EMBL- EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK Standards and infrastructure for managing experimental metadata Philippe Rocca-Serra,

EMBL-EBI EMBL-EBI EMBL-EBI What is the EBI's particular niche? Provides Core Biomolecular Resources in Europe –Nucleotide; genome, protein sequences,

ArrayExpress – a public database for microarray gene expression data Helen Parkinson Microarray Informatics Team European Bioinformatics Institute MGED.

MIAMExpress and the development of annotation ontologies for gene expression experiments Ele Holloway Microarray Informatics European Bioinformatics Institute.

A plant-specific annotation and submission tool for the incorporation of Arabidopsis gene expression data into ArrayExpress, the EBI’s public DNA microarray.

The UK eScience Grid (and other real Grids) Mark Hayes NIEeS Summer School 2003.

NERC Environmental Bioinformatics Centre Loading annotated spreadsheets into maxdLoad2.

Bio-Linux 3.0 An integrated bioinformatics solution for the EG community ClustalX showing DNA polymerase alignment GeneSpring showing yeast transcriptome.

Pedro: Combining Rapid Data Modelling and Ontology Services by Kevin Garwood E-Science North West Centre Manchester University.

Don’t make me think Biodiversity Data Publishing Made Easy Laurence Livermore, Vince Smith, Alice Heaton, Simon Rycroft, Ed Baker, Ben Scott & Lyubomir.

DMuDB: a shared mutation repository for UK diagnostic labs Andrew Devereau, Ed Burke.

EBI is an Outstation of the European Molecular Biology Laboratory. Tutorial 5: ChEBI - On-line Submission and Curation.

Ontology Driven Data Collection for EuPathDB Jie Zheng, Omar Harb, Chris Stoeckert Center for Bioinformatics, University of Pennsylvania.

EMBL- EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK The BioInvestigation Index – Standards and Infrastructure for Omics Data Philippe.

Information retrieval and sliding window programs April 5, 2011 Hand in Homework #1. Homework #2 due Tuesday, April 12. Learning objectives- Understand.

NERC Strategy Dave Tappin Unconventionals Workshop 24 th September 2014.

Systems Biology Tools for working with BIND data

Mangaldai College, Mangaldai

Subject repositories Session 6.3

Presentation transcript:

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) entries in Uniprot (Rel 14.9 – March 3, 2009) structures in PDB (March 3, 2009) experiments in GEO 7723 experiments in ArrayExpress entries in PubMed (March 9, 2009) 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

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.

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre Bio-Linux

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre Terminizer

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre Bioinvestigation Index and ISAcreator

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 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

NERC Environmental Bioinformatics Centre

NERC Environmental Bioinformatics Centre In practice… Data policy Standards Software Data management Support