MGED Ontology

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MGED Ontology

• Angel Pizarro
• Center for Bioinformatics, CBIL
• University of Pennsylvania

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Overview

• Goals
• In-depth look at the ontology
• Status Report

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MGED Ontology Goals

• Enable investigators to annotate experiments in a
  standardized way
• Enable programmers to create forms and generate
  MAGE documents with standardized terms (MGED Core
  Ontology)
• Enable communities to build on the MAGE Core
  Ontology (MGED Extended Ontology)
• Enable investigators to submit additional terms
  for the MGED Ontology

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The MGED Ontology Home Page
http//mged.sourceforge.net/ontologies/
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http//mged.sourceforge.net/ontologies
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Policies for Core Ontology(posted at web site)

• Organize ontology according to MAGE packages
• Class names have been changed to facilitate
  mapping and properties adjusted to avoid
  conflicts.
• Core ontology does not cover all of MAGE or
  contain all MAGE associations. Scope of ontology
  is supporting MAGE ontology entry associations,
  adding constraints within MAGE structure, and
  adding further structure and depth to MAGE
  classes without changing base classes.
• Definitions are derived from MAGE OMG document
  Gene Expression Specification where appropriate
  and available.
• Enumerated lists are represented as instances of
  a class where these lists are open ended.
• Classes not found in MAGE were moved to the
  extended ontology except in cases where
  subclasses are used to organize instances.
• When instances for a single class became
  numerous, subclasses to conceptually organize the
  instances were used.
• Associations not found in MAGE classes were
  removed.
• When simply an association to a controlled term
  list, the property "has_type" is used except in
  special MAGE cases such as has_biosample_type.
• When Ontology needed but no direct association,
  used describable (if describable) e.g.,
  transformation.
• For defining terms, include synonyms but indicate
  whether exact or non-exact.
• Term identifiers will be from DAML resource.
  i.e., http//mged.sourceforge.net/ontologies/MGEDO
  ntology.damlterm

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Current MGED Ontology
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MGED Ontology BioSequence
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ArrayExpress MAGE to MIAME mappinghttp//www.ebi.
ac.uk/ele/ext/submitter.html
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MGED Ontology BioMaterialPackage
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MGED Ontology OntologyEntry
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http//www.sofg.org
Currently a place holder with a link to the
meeting of Standards and Ontologies for
Functional Genomics (SOFG) but will be a home for
ontologies. Expect to see Anatomy soon.
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MGED Ontology ExperimentPackage
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How do you use it?

• As a term dictionary
• Reference the terms via MAGE OntologyEntry class
  through a stable URI
• Provide a mapping of MAGE to MIAME concepts
• To direct development and population of web-entry
  forms
• MIAMExpress (EBI)
• RAD Forms (CBIL)

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MGED Ontology Status Report

• Nov, 2002. SOFG meeting
• MGED Ontology v1.6 released
• Decision to create a MAGE-based Core Ontology
• Dec, 2002. Penn Ontology Workshop (POW) 1
• Helen P., Trish W., Chris S.
• First pass at Ontology 1.6 gt Core Ontology
• Jan, 2003. POW 2
• Cathy B., Paul S., Joe W., Helen P., Trish W.,
  Chris S.
• Review of Core, pretty much set
• created Ontology as Core Extended
• Started adding instances
• March 14-17 2003. Third Ontology Workshop
• Sept, 2003. Core Ontology finished and presented
  at MGED 6.

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Acknowledgements

• Christian Stoeckert (CBIL)
• Trish Whetzel (CBIL)
• Helen Parkinson (EBI)
• Paul Spellman
• Joe White (TIGR)
• Cathy Ball (Stanford)
• The rest of the Ontology Working Group
• http//mged.sourceforge.net/ontologies/index.php