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The MGED Ontology Workshop. MGED 7 September 8, 2004 Chris Stoeckert Center for Bioinformatics & Dept. of Genetics University of Pennsylvania. MGED Ontology Workshop Agenda. What is the MGED Ontology (MO)? Building MO: the process Using MO Future development of MO

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The mged ontology workshop

The MGED Ontology Workshop

MGED 7

September 8, 2004

Chris Stoeckert

Center for Bioinformatics & Dept. of Genetics

University of Pennsylvania


Mged ontology workshop agenda
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


Mged standardization efforts
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)


Mged ontology mo
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


Relationship of mo to mage om
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


Mged ontology class hierarchy
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




Main focus of mged ontology

BioMaterial

OntologyEntry

Main focus of MGED Ontology

  • Structured and rich description of BioMaterials

+characteristics

+associations





Standards and Ontologies for Functional Genomics 2October 23-26, 2004held at the University of Pennsylvania Medical Schoolwww.jax.org/courses/events

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




Mged ontology development http mged sourceforge net ontologies mgedontology php
MGED Ontology developmenthttp://mged.sourceforge.net/ontologies/MGEDontology.php

  • OILed

  • File formats

    • DAML file

    • HTML file

    • NCI DTS Browser

  • Changes

    • Notes

    • Term Tracker


Mged ontology working group
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


Desirable microarray queries
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?



RAD: RNA Abundance Databasehttp://www.cbil.upenn.edu/RAD

  • RADis 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 20:452-459.


RAD Study-Annotator

  • Covers all relevant parts of the MIAME checklist

  • Exploits the MGED Ontology

  • Allows entering of very specific details of an experiment

  • Web-based forms:

    • Modular structure

    • Written in PHP

    • Front-end data integrity checks using JavaScript

  • Manages Data Privacy based on Project/Group selections present in GUS schema

  • Available at http://www.cbil.upenn.edu/RAD/RAD-installation.htm



Rad study annotator biomaterial module
RAD Study Annotator: BioMaterial Module


Rad study annotator biosource form
RAD Study Annotator: BioSource Form


Other sites using mo
Other Sites Using MO

See posters for more details on these!


Future development of mo
Future Development of MO

  • Areas of Development

    • Ongoing maintenance

    • Ontology language

    • Non-array technologies

    • Biological domain extensions

    • MO v2. development


Proposed methods for mo development
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


Proposed methods for mo development1
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.


Proposed methods for mo development2
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).


A functional genomics view
A Functional Genomics View

Courtesy of Andy Jones


Proposed methods for mo development3
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!


Proposed methods for mo development4
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.


A functional genomics object model fge om
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


Proposed development of mged ontology
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


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