OBI Past

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OBI Past Present

• Chris Stoeckert
• University of Pennsylvania
• Jan 29th, 2007
• OBI Workshop
• La Jolla Institute for Allergy Immunology

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OBI Mission

• The Ontology for Biomedical Investigations (OBI)
  project is developing an integrated ontology for
  the description of biological and medical
  experiments and investigations. This includes a
  set of common' terms, that are applicable across
  various biological and technological domains, and
  domain-specific terms relevant only to a given
  domain. This ontology will support the consistent
  annotation of biomedical investigations,
  regardless of the particular field of study. The
  ontology will model the design of an
  investigation, the protocols and instrumentation
  used, the material used, the data generated and
  the type analysis performed on it.

http//obi.sourceforge.net/
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A Functional Genomics View
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OBI Timeline
MO/ MAGE
2004 2005 2006 2007
MAGE Jamboree Hinxton Dec
SOFG Philadelphia Oct
Transcriptomics (MGED) Proteomics (PSI)
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Standards and Ontologies for Functional Genomics
2October 23-26, 2004Philelphia, PA, USA
Co-Hosted by The Jackson Laboratory University
of Pennsylvania European Bioinformatics
Institute ------------------------
Funded in part by NHGRI NCRR NCI NIEHS-NCT NERC GS
K
Photo by R. Kennedy, B Trist, R. Tarver, for GPTMC
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OBI Timeline
MO/ MAGE
2004 2005 2006 2007
MAGE Jamboree Hinxton Dec
SOFG Philadelphia Oct
Transcriptomics (MGED) Proteomics (PSI)
Toxicogenomics Environmental Genomics Nutrigenomic
s (MGED RSBI)
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Relationship to FuGE-OM

• A Functional Genomics Object Model is under
  development.
• An unifying object model for different types of
  functional genomics experiments
• FuGO will provide ontology terms for FuGE
  wherever needed but not be dependent on the
  FUGE-OM
• FuGO will NOT emulate FuGE.
• True for other object models as well

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OBI Timeline
FuGO FuGE
MO/ MAGE
2004 2005 2006 2007
OBI Workshop San Diego Jan.
MAGE Jamboree Hinxton Dec
MGED 8 Bergen Sept.
MAGE Jamboree Stanford March
SOFG Philadelphia Oct
Transcriptomics (MGED) Proteomics (PSI)
PSI Siena April
Toxicogenomics Environmental Genomics Nutrigenomic
s (MGED RSBI)
Cellular Assays Immport IEDB
Neuroinformatics
Metabolomics Flow Cytometry
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OBI Communities

• Bioimaging Coordinator Daniel Rubin, Jeff Grethe
• Cellular Assays Coordinator Stefan Wiemann
• Clinical Trial Coordinator (Barry Smith)
• Crop Sciences Coordinator Richard Bruskiewich
• Environmental Genomics Coordinator Dawn Field
• Flow Cytometry Coordinator Ryan Brinkman
• Genomics Coordinators Dawn Field, Tanya Gray
• ImmPort Coordinator Richard Scheuermann
• Immune Epitope Database and Analysis Resource
  Coordinator Bjoern Peters
• In Situ Hybridization and Immunohistochemistry
  Coordinator Eric Deutsch
• Metabol/nomics Coordinators Susanna Sansone,
  Daniel Schober
• Neuroinformatics and Bio-imaging Coordinator
  Bill Bug
• Nutrigenomics Coordinator Philippe Rocca-Serra
• Polymorphism Coordinator Tina Hernandez-Boussard
• Proteomics Coordinators Luisa Montecchi, Susanna
  Sansone, Daniel Schober, Chris Taylor, Trish
  Whetzel
• Toxicogenomics Coordinator Jennifer Fostel
• Transcriptomics Coordinators Helen Causton, Liju
  Fan, Jennifer Fostel, Gilberto Fragoso, Mervi
  Heiskanen, Helen Parkinson, Philippe Rocca-Serra,
  Susanna Sansone, Chris Stoeckert, Trish Whetzel,
  Joe White

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OBI Organization
OBI Coordinating Committee
Advisory Board
OBI Developers
Frank Hartel Suzi Lewis Mark Musen Steve
Oliver Barry Smith Robert Stevens
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OBI Hierarchy Structure
Coordinators Developers Advisors

• Funding
• community participation
• put effort into OBI
• attending and hosting workshops
• coordination
• MGED Trish Whetzel

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OBI Accomplishments

• Infrastructure
• Policy document for project (OBI-GroupsRegs_v0.2.d
  oc)
• Information distributed through Wiki,
  sourceforge, and email lists.
• Conference calls (mothly coordinators and weekly
  developers) and face-to-face workshops (biannual)
• Ontology tools (Protégé, OWL) and design
  principles (OBO Foundry)
• Ontology
• Collected community use cases
• Collected community terms (e.g., data
  transformation)
• Upper level ontology (Basic Formal Ontology)
• Initial population of common terms

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OBI Next Steps

• Development
• Integration with BFO and OBO
• and establish formally how OBI stands with other
  related efforts
• Add terms directly related to investigations that
  are common to multiple communities
• and provide a working draft that each community
  can build on
• Outreach
• Describe our efforts and results in our current
  communities
• and get feedback and buy-in
• Identify and recruit communities that fill in
  major unrepresented domains
• and establish OBI as the defacto resource for
  annotating biomedical investigations

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FuGO status

• Set up committees
• Community coordination
• Developers
• Advisory Board
• Reviewed use cases from different communities
• Collected top 50 terms from communities
• Philadelphia Workshop created an upper level
  ontology
• Voted to become an OBO Foundry Application
  Ontology
• Paper forthcoming in Omics Journal special issue
  on standards and ontologies
• Note Also a parallel FuGE effort analogous to
  MAGE that will use FuGO.

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Functional Genomics Experiment - Object Model
Namespaces
Components common to all functional genomics
experiments
Top-level of the Object Model
MAGE-OM derived
Microarray specfic components
Classes modelling proteomics technologies
PEDRo and Gla-PSI derived