Exploiting scientific data in the domain of omics

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Exploiting scientific data in the domain of omics

• 'Genomics Standards Consortium
• Ontology requirements and experiences'

Dawn Field Oxford Centre for Ecology and Hydrology
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Overview

• Goal of this Workshop to explore what's been
  achieved to date with RDF, meta-data and
  ontologies in exploiting scientific data -
  particularly data integration, discovery and
  sharing
• what we have achieved
• the challenges we face
• what we hope to achieve in the near future
• what are the major issues requiring further
  research

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Challenges and Opportunities

• Rapidly growing collection of genomes
• Increasing need for researchers to access,
  combine and analyze data sets containing genomic,
  taxonomic, ecological and environmental data
• Increasing number of initiatives capturing
  metadata
• Additional information about complete genome
  sequences would be beneficial

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De novo DNA sequencing Continues to grow
exponentially
SymBio Corporation
SymBio Corporation
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Data scope of genome resources at NCBI
Environmental samples?
Organisms
Nematoda
C.elegans, C.briggsae
Microbes
Viruses
Fungi/small eukaryotes
Plants
A.thaliana Barley Corn Oat Rice Soybean Tomato Ric
e Wheat
Fishes
Insects
D.melanogaster, A.gambia, D.pseudoobscura, Honey
bee,
Chicken
Dog
Mouse/Rat
pig, cow
Human
chimpanzee
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The Promise of Metagenomics
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Features of GBMF marine microbial genome
sequencing project webpage ? Acts as portal
to primary investigator webpage ? Provides
basic information about the organism 1)
Phylogeny of organism 2) Physiology, if
known 3) Habitat 4) Geographic
location 5) Isolation technique 6) Primary
citation 7) Culture collection
www.moore.org/microgenome
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Problems

• DATA INTEGRATION!!!!!
• NO SUFFICIENT DATA REGARDING PHYSIOLOGY OF
  ORGANISMS !!!!

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Morphology and Growth

• Haemophilus influenzae is a non-motile,
  gram-negative, rod shaped bacterium. Optimal
  growth temperature is 37 degrees and doubling
  time in culture is 26 minutes.

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Interactions and Ecology

• H. influenzae is a obligate commensal with the
  ability to cause disease including menigitis and
  otitis media. The primary habitat of this species
  is the human nasopharyx. This bacterium is
  faculatively anaerobic and uses organic matter as
  a source of carbon and organic matter as a source
  of energy.

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What we have achieved
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Cataloguing our Complete Genome Collection

• Proposal Field D, Hughes J (2005). Cataloguing
  our current genome collection. Microbiology 151
  1016-1019
• Analysis Hughes J Field D (2005) Ecological
  Perspectives on our complete genome collection
  Ecology Letters. 8, 1334-1345
• Workshop Cataloguing our current genome
  collection Sept 7-9, 2005 Cambridge, UK NIEeS
  D. Field, G. Garrity, N. Morrison, J. Selengut,
  P. Sterk, N. Thomson, T. Tatusova. Meeting
  report. Comp. Func. Genomics.
• Genomic Standards Consortium (GSC)
  http//gensc.sourceforge.net
• Funding Cataloguing our current genome
  collection (NERC International Opportunities
  Fund Award NE/3521773/1)

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Cataloguing our Complete Genome Collection

• Workshop Cataloguing our current genome
  collection II Nov 10-11, 2005, EBI, Cambridge,
  UK D. Field, N. Morrison, J. Selengut, P. Sterk,
  Meeting report OMICS (in press)
• Special issue of OMICS on data standards guest
  editors Dawn Field and Susanna Sansone organized
  around first two GSC workshops
• Funding Cataloguing our current genome
  collection funding from NIEeS for two more
  workshops in June 2006 and 2007
• Workshop 3rd GSC workshop Sept 11-13, 2006
  NIEeS, Cambridge UK. Co-organizers Dawn Field and
  Tatiana Tatusova
• Genome Catalogue Launch of implementation of
  MIGS checklist as a database ready to accept case
  study genomes

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Overview of GSC activities

• The aim of the Genomic Standards Consortium (GSC)
  is to support the
• community-based development of a genomic standard
  that captures a
• richer set of information about complete genomes
  and metagenomic
• datasets.
• Checklist
• Implementation
• Ontology development
• Metadata exchange

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Overview of GSC activities

• Checklist The GSC is currently working together
  towards the "Minimal Information about a Genome
  Sequence" (MIGS) specification.
• Implementation To promote discussion and support
  the capture of preliminary data an XML schema has
  been built from the checklist and implemented as
  the Genome Catalogue database.

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Overview of GSC activities

• Ontology development The GSC is also working
  towards the development of controlled
  vocabularies for describing genomes and this work
  feeds into the FuGO project (A Functional
  Genomics Investigation Ontology).
• Metadata exchange GFF3 and GnoME

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The challenges we face
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Challenges

• Defining the standard
• Collecting the data
• Fields can be calculated in a variety of ways
  separate curated and calculated fields
• We dont know enough about many of these genomes
  with respect to lifestyle
• Relationships between genomes
• Completeness of data

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Defining the Checklist
Concepts Organism Phenotype Environment Sample
Processing Data Processing
Taxonomic Groups Eukaryotes Bacteria/Archaea Plas
mids Viruses Organelles Metagenomes
Implementation Working Group Metadata Exchange
Working Group
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Proliferation of MI Checklists

• Upcoming special issue of OMICS a journal of
  integrative biology on data standards includes
  descriptions of 7 checklists
• Upcoming issue of Nature Biotechnology expected
  to include more

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Protein Standards Initiative (June 2006)Special
sessionThe proliferation of MI checklists
opportunities and challenges

• Chris Taylor (EBI) Minimal Information about a
  Protein Experiment (MIAPE) and MIxxx and the
  need for a central registry
• Dawn Field (CEH Oxford) Minimal Information about
  a Genome Sequence (MIGS)
• Don Robertson (Pfizer Global RD, Ann Arbor MI)
  MSI -- Metabolomics Standards Initiative.
• Graeme Grimes (Scottish Centre for Genomic
  Technology and Information, Edinburgh, UK)
  Minimum Information About a RNAi Experiment
  (MIARE)
• Stefan Wiemann (DKFZ, Heidelberg, Germany)
  Minimum Information About a Cellular Assay
  (MIACA)
• Ryan Brinkman (UBC, Canada) presented by Chris
  Taylor (EBI) Minimum Information for a
  Fluorescence Activated Cell Experiment (MIFACE)

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• MICheck A Minimum Information Checklist Portal
• Chris Taylor, Dawn Field, Susanna-Assunta
  Sansone, Rolf Apweiler, Michael Ashburner, Cathy
  Ball, Pierre-Alain Binz, Alvis Brazma, Ryan
  Brinkman, Eric Deutsch, Oliver Fiehn, Jennifer
  Fostel, Peter Ghazal, Graeme Grimes, Nigel Hardy,
  Henning Hermjakob, Randall Julian, Martin Kuiper,
  Nicholas Le Novère, Jim Leebens-Mack, Suzi Lewis,
  Ruth McNally, Norman Morrison, Norman Paton, John
  Quackenbush, Donald Robertson, Philippe
  Rocca-Serra, Barry Smith, Jason Snape, Stefan
  Wiemann

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micheck.sourceforge.net

• The MICheck website will provide
• a comprehensive list of MI checklists
• convenience links to relevant resources
  appropriate tools, data formats, ontologies
• links to relevant policy statements from various
  external bodies (such as funders data sharing
  policies, journals publication guidelines and so
  forth).
• contact(s) for submitting feedback
• where possible, most recent versions of
  checklists (either as a local copy or a link)
• charter for the group
• guidelines for registering a checklist
• sign-up details for the mailing list.

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micheck.sourceforge.net

• The MICheck website will provide
• Minimal Information about a Minimal Information
  Checklist (MIMI)
• Searchable database of terms from all checklists

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We propose that the MICheck play two primary
roles

• The first is to provide a one-stop shop for
  researchers, journal editors and reviewers, and
  funders providing a quick and simple way to
  discover (whether there are) guidelines for a
  particular domain.
• This second is to facilitate investigation of the
  boundaries, overlaps and gaps between projects,
  minimally by raising awareness of the scope and
  progress of extant efforts.

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These two roles translate into two distinct parts
of MICheck

• Portal exists simply to raise awareness of, and
  afford simple access to a wide range of
  checklists registering for the portal implies no
  commitment to integrate by the registrant.
• Foundry communities can, if motivated, sign up
  to the foundry to jointly examine ways to
  refactor the checklists over which they have
  control and begin to produce the first components
  of a suite of self-consistent, clearly bounded,
  orthogonal, integrable checklist modules.

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Registering a project

• Domain Genomics and metagenomicsChecklist
  type Primary guidelinesCommunity Name The
  Genomic Standards ConsortiumMain website
  http//gensc.sourceforge.org/MI Checklist Name
  Minimal Information about a Genomic SequenceMI
  Checklist Acronym MIGSCurrent Version Number
  0.1Release Date for current version
  2006-01-01Primary Contact Person Dr Jane
  DoeComments Early draft based on first two
  exploratory workshops public distribution for
  commentKey concepts eukaryotes,
  bacteria/archaea, plasmids, organelles, viruses,
  metagenomes, organism, phenotype,
  environment, sample processing, data
  processingBibliography Publications to be
  reposited where possibleLocation of document(s)
  http//sourceforge.net/project/showfiles.php?group
  _id153365

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Proteomics three main efforts

• The Minimum Information About a Proteomics
  Experiment (MIAPE)
• HUPO Proteomics Standards Initiative
• The Paris Guidelines
• sponsored by MCP
• Guidelines for the Next Ten Years of Proteomics
• published by Proteomics

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Integrative Activities
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Defining the Checklist
Investigation
Concepts Organism Phenotype Environment Sample
Processing Data Processing
Taxonomic Groups Eukaryotes Bacteria/Archaea Plas
mids Viruses Organelles Metagenomes
Study
Assay
Implementation Working Group Metadata Exchange
Working Group
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what we hope to achieve in the near future
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FuGO An Ontology for Functional Genomics
Investigation
Susanna-Assunta Sansone (EBI) Overview Trish
Whetzel (Un of Penn) Microarray Daniel Schober
(EBI) Metabolomics Chris Taylor (EBI)
Proteomics On behalf of the FuGO working
group http//fugo.sourceforge.net
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FuGO - Rationale

• Standardization activities in (single) domains
• Reporting structures, CVs/ontology and exchange
  formats
• Pieces of a puzzle
• Standards should stand alone BUT also function
  together
• - Build it in a modular way, maximizing
  interactions
• Capitalize on synergies, where commonality
  exists
• Develop a common terminology for those parts of
  an investigation that are common across
  technological and biological domains

                                       
 
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FuGO - Overview

• Purpose
• NOT model biology, NOR the laboratory workflow
• BUT provide core of universal descriptors for
  its components
• To be extended by biological and technological
  domain-specific WGs
• No dependency on any Object Model
• - Can be mapped to any object model, e.g. FuGE OM
• Open source approach
• Protégé tool and Ontology Web Language (OWL)

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FuGO Communities and Funds

• List of current communities
• Omics technologies
• HUPO - Proteomics Standards Initiative (PSI)
• Microarray Gene Expression Data (MGED) Society
• Metabolomics Society Metabolomics Standards
  Initiative (MSI)
• Other technologies
• Flow cytometry
• Polymorphism
• Specific domains of application
• Environmental groups (crop science and
  environmental genomics)
• Nutrition group
• Toxicology group
• Immunology groups
• List of current funds
• NIH-NHGRI grant (C. Stoeckert, Un of Pen) for
  workshops and ontologist
• BBSRC grant (S.A. Sansone, EBI) for ontologist

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FuGO Processes

• Coordination Committee
• Representatives of technological and biological
  communities
• - Monthly conferences calls
• Developers WG
• Representatives and members of these communities
• - Weekly conferences calls
• Documentations
• http//fugo.sourceforge.net
• Advisory Board
• Advise on high level design and best practices
• Provide links to other key efforts
• Barry Smith, Buffalo Un and IFOMIS
• Frank Hartel, NIH-NCI
• Mark Musen, Stanford Un and Protégé Team
• Robert Stevens, Manchester Un
• Steve Oliver, Manchester Un
• Suzi Lewis, Berkeley Un and GO

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FuGO Strategy

• Use cases -gt within community activity
• Collect real examples
• Bottom up approach -gt within community activity
• Gather terms and definitions
• - Each communities in its own domain
• Top down approach -gt collaborative activity
• Develop a naming convention
• Build a top level ontology structure, is_a
  relationships
• Other foreseen relationships
• - part_of (currently expressed in the taxonomy as
  cardinal_part_of)
• - participate_in (input) and derive_from
  (output),
• - describe or qualify
• located_in and contained_in
• Binning terms in the top level ontology
  structure
• The higher semantics helps for faster binning

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FuGO Status and Plans

• Binning process - ongoing
• Reconciliations into one canonical version
• Iterative process
• Common working practices - established
• Each class consists of term ID, preferred
  term, synonyms, definition and comments
• Sourceforge tracker to send comments on terms,
  definitions, relationships
• Timeline for completion of core omics
  technologies
• Two years and several intermediate milestones
• Interim solution
• - Community-specific CVs posted under the OBO
• Ultimately FuGO will be part of the OBO Foundry
  (Core) Ontology
• Overview paper Special Issue on Data
  Standards OMICS journal

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Areas requiring significant research
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Summary gensc.sf.net

• The GSC is tackling the issue of describing our
• complete genome collections in greater detail
• through
• MIGS
• Genome Catalogue
• Ontology Development
• Metadata Exchange
• In co-ordination with
• MICheck micheck.sf.net
• FuGO fugo.sf.net

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Acknowledgements

• GSC Coordinators
• Dawn Field (CEH Oxford)
• George Garrity (Bergeys Trust)
• Norman Morrison (NEBC)
• Jeremy Selengut (TIGR)
• Peter Sterk (EBI)
• Tatiana Tatusova (NCBI)
• Nick Thomson (Sanger)

Working Groups General Members of the
GSC Participants of all meetings
gensc.sf.net
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Acknowledgements

• MICheck A Minimum Information Checklist Portal
• Chris Taylor, Dawn Field, Susanna-Assunta
  Sansone, Rolf Apweiler, Michael Ashburner, Cathy
  Ball, Pierre-Alain Binz, Alvis Brazma, Ryan
  Brinkman, Eric Deutsch, Oliver Fiehn, Jennifer
  Fostel, Peter Ghazal, Graeme Grimes, Nigel Hardy,
  Henning Hermjakob, Randall Julian, Martin Kuiper,
  Nicholas Le Novère, Jim Leebens-Mack, Suzi Lewis,
  Ruth McNally, Norman Morrison, Norman Paton, John
  Quackenbush, Donald Robertson, Philippe
  Rocca-Serra, Barry Smith, Jason Snape, Stefan
  Wiemann

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FuGO An Ontology for Functional Genomics
Investigation
Susanna-Assunta Sansone (EBI) Overview Trish
Whetzel (Un of Pen) Microarray Daniel Schober
(EBI) Metabolomics Chris Taylor (EBI)
Proteomics On behalf of the FuGO working
group http//fugo.sourceforge.net