Transcriptomics Community Introduction

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Transcriptomics Community Introduction

• Trish Whetzel
• University of Pennsylvania
• On behalf of the
• MGED Society/MGED Ontology Working Group

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Who are we?

• The Transcriptomics Community includes
• Individuals that generate and annotate
  MIAME-compliant microarray data using the MGED
  Ontology and MAGE related formats (MAGE-ML,
  MAGE-TAB)
• Represented in OBI by members of the MGED
  Ontology Working Group
• Helen Causton, Liju Fan, Gilberto Fragoso, Mervi
  Heiskanen, Helen Parkinson, Susanna Sansone,
  Philippe Rocca-Serra, Chris Stoeckert

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What are we currently doing with ontologies?

• MGED Ontology (MO)
• Developed to annotate microarray data
• Includes the experiment design and factors,
  protocols, biomaterials, and results and analysis
• In use in production annotation systems
• Array Express, BuG_at_Sbase, CaArray, CEBS, maxd,
  MiMiR, RAD Study-Annotator, Stanford Microarray
  Database, Tox-MIAMExpress

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What are we currently doing with ontologies?

• Activities Related to MO
• Re-factoring of MO - add unique identifiers for
  all terms, implementing a term deprecation
  policy, etc.
• Maintaining MO - adding new terms, synonyms
• Developing a term tracker and web services to
  better utilize and manage MO
• Re-factoring this resource through the
  development/contribution to OBI and other OBO
  Foundry ontologies (PATO, Unit ontology)

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What are our plans?

• MGED Ontology will continue to exist indefinitely
• Continue to add new terms
• Improve the applicability of MO
• Contribute MO terms for inclusion in OBI
• Provide mapping file between MO and OBI
• Facilitate use of OBI by the Transcriptomics
  community
• Data annotations are comparable annotated with
  either resource

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What are our goals for the workshop?

• Develop timeline for deliverables for OBI
  development
• Agree to community authoring policy and topics to
  work on in OBI
• Incorporate MO terms into OBI
• Specifically, Data Transformation and
  Investigation terms
• Generally, remaining terms in MO

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What can the Transcriptomics Community Contribute?

• Experience from building and using the MGED
  Ontology
• Experience in building databases and annotation
  tools that incorporate ontology terms
• Experience with data standards (checklists,
  object models) that use ontologies
• Experience of using an OM and an ontology

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Transcriptomics Community Requirements for FuGO?

• An ontology that provides terms, relations, and
  restrictions that are both universal and
  array-specific, therefore ability to support the
  annotation needs of data expressed in FuGE and
  MAGEv2
• Mechanism to grab universal and transcriptomics
  specific terms
• An ontology that is map-able to MO

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Challenges?

• Accessible to presentation framework, ability to
  map between ontology and object model for use in
  annotation software
• Address the need for terms to describe higher
  level analysis and quality control processes
• Migration and/or mapping of data annotated with
  MO to data annotated with FuGO
• Mapping from data annotated using something other
  than MO to FuGO, e.g. data from GEO

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Transcriptomics Members participating in FuGO
Workshop

• Helen Causton
• Liju Fan
• Gilberto Fragoso
• Mervi Heiskanen
• Helen Parkinson
• Susanna Sansone
• Philippe Rocca-Serra
• Chris Stoeckert
• Trish Whetzel

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