Microarray Gene Expression Database (MGED) Ontology Working Group Chris Stoeckert Center for...
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Transcript of Microarray Gene Expression Database (MGED) Ontology Working Group Chris Stoeckert Center for...
![Page 1: Microarray Gene Expression Database (MGED) Ontology Working Group Chris Stoeckert Center for Bioinformatics University of Pennsylvania July 26, 2001.](https://reader036.fdocuments.in/reader036/viewer/2022062800/56649dfe5503460f94ae615d/html5/thumbnails/1.jpg)
Microarray Gene Expression Database (MGED) Ontology
Working Group
Chris Stoeckert
Center for Bioinformatics
University of Pennsylvania
July 26, 2001
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http://www.mged.org
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MGED Steering Committee
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MGED Working Groups
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MIAME v1.0
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MIAME section onsample source andtreatment
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MAGE Object Model
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MAGE BioMaterial Model
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MGED OWGhome page
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OWG Use Cases• Return a summary of all experiments that use a
specified type of biosource.– Group the experiments according to treatment.
• Return a summary of all experiments done examining effects of a specified treatment– Group the experiments according to biosource.
• Return a summary of all experiments measuring the expression of a specified gene.– Indicate when experiments confirm results, provide new
information, or conflict.
• Generate a distance metric for experiment types• Generate an error estimation for experimental
descriptions
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OWGSampleConcepts
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SpeciesResources
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ConceptDefinitions
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Excerpts from a Sample Descriptioncourtesy of M. Hoffman, S. Schmidtke, Lion BioSciences
Organism: mus musculus [ NCBI taxonomy browser ]Cell source: in-house bred mice (contact: [email protected]) Sex: female [ MGED ]Age: 3 - 4 weeks after birth [ MGED ]Growth conditions: normal
controlled environment20 - 22 oC average temperaturehoused in cages according to German and EU legislationspecified pathogen free conditions (SPF)14 hours light cycle10 hours dark cycle
Developmental stage: stage 28 (juvenile (young) mice) [ GXD "Mouse Anatomical Dictionary" ]Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ]Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice]Genetic Variation: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ]Treatment: in vivo [MGED] intraperitoneal injection of Dexamethasone into mice, 10 microgram per 25 g bodyweight of the mouseCompound: drug [MGED] synthetic glucocorticoid Dexamethasone, dissolved in PBS
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Biomaterial Concepts• Environmental or experimental history: A description of the conditions the
organism has been exposed to that are not one of the variables under study. – Culture conditions: A description of the isolated environment used to grow
organisms or parts of the organism. • atmosphere, humidity, temperature • light: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
• nutrients: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS,
etc.). • medium: The physical state or matrix used to provide nutrients to the organism (e.g.,
liquid, agar, soil) • density range: The concentration range of the organism. • contaminant organisms: Organisms present that were not planned as part of the study
(e.g., mycoplasma). • removal of contaminants: Steps taken to eliminate contaminant organisms. • host organism or organism parts: Organisms or organism parts used as a designed
part of the culture (e.g., red blood cells, stromal cells).
– Generations: The number of cell divisions if the organism or organism part that is cultured is unicellular otherwise the number of breedings.
– Clinical history: The organism's (i.e., the patient's) medical record. – Husbandry: water, bedding, barrier facility, pathogen test results– Preservation: seed dormancy, frozen storage
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Biomaterial Concepts• Treatment: The manipulation of the biomaterial for the purposes
of generating one of the variables under study. – somatic modification: The organism has had parts removed, added,or
rearranged. – genetic modification: The organism has had genes removed, added, or
rearranged.– starvation: The organism (or organism part) has been deprived of nutrients. – infection: The organism (or organism part) has been exposed to a virus or
pathogen. – behavioral stimulus: The organism is forced to respond to a stimulus with some
behavior (e.g., avoidance, obtaining a reward, etc.) – agent-based treatment: The treatment is effected by a defined chemical,
biological, or physical agent.
– agent type: chemical (drugs), biological (macromolecule), physical (stress from light, temperature, etc.)
• agent application: In vivo, in vitro, in situ; qualitative or quantitative– treatment protocol: method of treatment – treatment parameters: constant, variable – treatment duration: length of treatment
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Biomaterial Concepts• Biomaterial preparation: A description of the state
and condition of the biomaterial. – Time of day when the biomaterial was generated (i.e.,
sampled). Pathological staging: pre or post mortem at sampling
– state at start of treatment (age, time of day) – physio-chemical composition of the sample: amount of
material, number of cells, purity. – Extraction: Chemical extraction, Physical extraction – protocol: method used. – Pool types:
• Multiple: Biomaterial prepared from multiple specimens, but same Organism, Genotype, Phenotype and treatment.
• Individually: Biomaterial prepared from individually specimen, but same Organism, Genotype, Phenotype and treatment
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Ontology Working Group
1. Identify concepts
2. Collect available controlled vocabularies and ontologies for concepts
3. Define concepts
4. Formalize concept relationships
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Generating a Usable Microarray Ontology
Make it accessible.Make it now.Make it consistent.Class (isa) and attributes (part-of)
– Taxonomic hierarchies– Directed acyclic graphs
Graph with labeled edges– Rules and integrity constraints
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Current Plans
• Provide concepts and definitions along with sources of controlled terms
• Continue collecting examples of sample descriptions– Using MGED list – From existing databases
• Begin structuring concepts common to all biomaterials– Environment, history, treatment– Start with MIAME, MAGE OM
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ConceptDefinitions
*
*
*
*
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Future
• Provide a usable ontology for microarrays– Not just sample descriptions– Incorporate organism-specific name spaces
• Generate an object model for concepts– Rectify with MAGE– Use to build databases
• Generate XML– Use to populate databases
• First draft by MGED 4 (Feb., 2002)
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MGED-Related sites
• MGED: http://www.mged.org
• MIAME: http://www.mged.org/Annotations-wg/
• MAGE: http://www.geml.org/omg.htm
• OWG: http://www.cbil.upenn.edu/Ontology