The MGED Ontology Workshop

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The MGED Ontology Workshop

• MGED 7
• September 8, 2004
• Chris Stoeckert
• Center for Bioinformatics Dept. of Genetics
• University of Pennsylvania

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MGED Ontology Workshop Agenda

• What is the MGED Ontology (MO)?
• Building MO the process
• Using MO
• Future development of MO
• Joe White (TIGR) MO applications from MAGE
  Jamboree

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MGED Standardization Efforts

• MIAME
• The formulation of the minimum information about
  a microarray experiment required to interpret and
  verify the results. (Brazma et al. Nature
  Genetics 2001)
• MAGE-OM
• The establishment of a data exchange format and
  object model for microarray experiments.
  (Spellman et al. Genome Biol. 2002)
• MGED Ontology
• The development of an ontology for microarray
  experiment description and biological material
  (biomaterial) annotation in particular. (Stoeckrt
  Parkinson, Comp. Funct. Genom. 2003)
• Transformations
• The development of recommendations regarding
  microarray data transformations and normalization
  methods.
• RSBI
• Reporting Structure for Biological Investigations
  (toxicogenomics, environmental genomics,
  metabol/nomics)

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MGED Ontology (MO)

• Purpose
• Provide standard terms for the annotation of
  microarray experiments
• Not to model biology but to provide descriptors
  for experiment components
• Benefits
• Unambiguous description of how the experiment was
  performed
• Structured queries can be generated
• Ontology concepts derived from the MIAME
  guidelines/MAGE-OM
• Also incorporating concepts from Transformations
  and RSBI

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Relationship of MO to MAGE-OM

• MO class hierarchy follows that of MAGE-OM
• Association to OntologyEntry
• MO provides terms for these associations by
• Instances internal to MO
• Instances from external ontologies
• Take advantage of existing ontologies

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MGED Ontology Class Hierarchy

• MGED CoreOntology
• Coordinated development with MAGE-OM
• Ease of locating appropriate class to select
  terms from
• MGED ExtendedOntology
• Classes for additional terms as the usage of
  genomics technologies expand

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MAGE and MO
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MAGE and MO
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Main focus of MGED Ontology

• Structured and rich description of BioMaterials

characteristics
associations
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MO and References to External Ontologies
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MO and references to External Ontologies
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http//www.sofg.org
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Standards and Ontologies for Functional Genomics
2October 23-26, 2004held at the University of
Pennsylvania Medical Schoolwww.jax.org/courses/ev
ents
Co-Hosted by The Jackson Laboratory University
of Pennsylvania European Bioinformatics
Institute ------------------------
Student Scholarships Available -------------------
-------------------------------------
Funded in part by NHGRI NCRR NERC GSK
Photo by R. Kennedy, B Trist, R. Tarver, for GPTMC
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http//mged.sourceforge.net/ontologies/index.php
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Use MGED Ontology for Structured Descriptions
(MAGE-ML)
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MGED Ontology developmenthttp//mged.sourceforge.
net/ontologies/MGEDontology.php

• OILed
• File formats
• DAML file
• HTML file
• NCI DTS Browser
• Changes
• Notes
• Term Tracker

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MGED Ontology Working Group

• Virtual Ontology Workshops
• Chris Stoeckert, Trish Whetzel (Penn)
• Helen Parkinson, Susanna Sansone (EBI)
• Joe White (TIGR)
• Gilberto Fragoso, Liju Fan, Mervi Heiskanen (NCI)
• Helen Causton, Laurence Game (ICL)
• Chris Taylor (PSI, EBI)
• Mged-ontologies mailing list

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Desirable Microarray Queries

• Return all experiments with species X examined at
  developmental stage Y
• Sort by platform type
• Which are untreated? Treated?
• Treated with what compound?
• How comparable are these?
• What can these experiments tell me?

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MO and Structured Queries
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RAD RNA Abundance Database http//www.cbil.upenn.
edu/RAD
RAD is part of GUS (Genomics Unified Schema) The
GUS platform maximizes the utility of stored data
by warehousing them in a schema that integrates
the genome, transcriptome, gene regulation and
networks, ontologies and controlled vocabularies,
gene expression Relational schema (implemented in
Oracle) Stores data from gene expression arrays
and SAGE Comes with a suite of web-annotation
forms (Study-Annotator) MAGE-RAD Translator
(MR_T) generates MAGE-ML files for
exports Manduchi et al. 2004 Bioinformatics
20452-459.
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BioMaterial Annotation Conceptual View
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RAD Study Annotator BioMaterial Module
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RAD Study Annotator BioSource Form
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Other Sites Using MO
See posters for more details on these!
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Future Development of MO

• Areas of Development
• Ongoing maintenance
• Ontology language
• Non-array technologies
• Biological domain extensions
• MO v2. development

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Proposed methods for MO development

• Ongoing maintenance
• Addition of new instance terms to existing
  classes
• Fixing typographical errors
• Adding missing associations
• These represent minor changes that should largely
  not affect software applications that are based
  on the MO

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Proposed methods for MO development

• Ontology language
• Planned changes in the primary language format
  (from DAML to OWL).
• Planned changes in the primary ontology editing
  tool (from OILed to Protégé).
• These should represent fairly minor differences
  as far as applications based on the MO are
  concerned.
• Some minor name changes will be needed to adjust
  for differences in allowed characters.
• New functionalities such as the availability of
  synonyms may be used to enrich the MO further.

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Proposed methods for MO development

• Non-array technologies
• Standards efforts for proteomics (PSI) and
  metabol/nomics (SMRS) would like to add terms for
  their specific needs.
• Classes that are needed for new technologies can
  be placed under the MGEDExtendedOntology and
  linked to MGEDCoreOntology classes through
  properties
• (i.e., MGEDExtendedOntologyClass has_property
  (MGEDCoreOntologyClass).
• Such development would not impact the
  MGEDCoreOntology and therefore allow addition of
  non-array technology classes
• Instances that are needed for new technologies
  may be most appropriate for existing classes in
  the MGEDCoreOntology
• The policy for adding and defining instances
  regarding technology-related terms is to provide
  a generic name and definition but to supply
  technology-specific examples (in the definition).

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A Functional Genomics View
Courtesy of Andy Jones
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Proposed methods for MO development

• Biological domain extensions
• Areas (e.g., toxicogenomics) where the current
  specification of Experiment and Biomaterial is
  not sufficient to fully capture descriptions of
  experiments
• Extensions should fit within the MAGE-OM v1.1 and
  so ultimately could go into the MGEDCoreOntology.
  
• However, as the new classes, subclasses,
  properties, and instances are under development
  (and therefore not stable), they should be placed
  in the MGEDExtendedOntology until mature enough
  to be migrated over to the MGEDCoreOntology.
• The MGED Reporting Structure for Biological
  Investigations (RSBI)Working Group representing
  biological domain extensions in toxicogenomics,
  environmental genomics, and nutrigenomics will
  take this approach.
• Hear more about this from Jennifer Fostel next!

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Proposed methods for MO development

• MO v2 development
• Reflect the reorganization planned for the
  MAGE-OM and its new major version (v2).
• MAGE v2 will have major structural changes from
  MAGE v1.1 and is likely to require major changes
  in the MO.
• With a MO v2 developed in parallel this should
  not conflict with the stated plans of the MO to
  be consistent with MAGE as it will be tied to the
  new version.

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A Functional Genomics Object Model (FGE-OM)

• Separate out common components from
  technology-specific ones
• Allow new domains to be added as new modules to
  the model
• Incorporate ideas from SysBio-OM (Xirasgur et al.
  Bioinformatics in press)

Jones et al. Bioinformatics 2004
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Proposed Development of MGED Ontology
MO 1.x
Move to OWL/Protege
Proteomics in ExtendedOntology
RSBI in ExtendedOntology RSBI in CoreOntology
MO 2.x
Sept. 2004 Jan. 2005 March 2005
Sept. 2005