Ontology Working Group


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"The MGED Ontology"

Ontology Container Information

Title:

"The MGED Ontology"

Classes:

233

Creator:

Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor

Properties:

143

Subject:

An ontology for microarray experiments in support of MAGE v.1.

Individuals:

681

Description:

Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1

Axioms:

Date:

Feb. 9, 2007

Version:

"1.3.1.1"

Note that this page now reflects the latest version 1.3.1.1. The previous verion (1.2.0) displayed is still available as an OWL file (see link below)

Deprecated Biosequence terms

Several of the MO BioSequence Terms have been deprecated as they map directly to the Sequence Ontology terms. A mapping file for the MO to SO terms is available.

Notes and edits to MO 1.3

Notes files for changes in MO version 1.3.0 and MO version 1.3.1.

Notes and edits to MO 1.2

A notes file containing edits, bug fixes, and additions is provided to document changes.

Notes and edits to MO 1.1.7/8/9

A notes file containing edits, bug fixes, and additions is provided to document changes.

Ontology terms under review

A tracker on sourceforge has been set up for new terms.

Alternate views of the MGED Ontology

Gilberto Fragoso has adapted the MGED Ontology to be viewed using the NCI DTS Browser. This provides a class view and explicitly shows inerited properties.
A static view of the class hierarchy can be found here.

Files

OWL: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#
OWL (previous version 1.3.0.1): http://mged.sourceforge.net/ontologies/MGEDOntology.1.3.0.1.owl#
OWL (previous version 1.2.0): http://mged.sourceforge.net/ontologies/MGEDOntology.1.2.0.owl#
OWL (previous version 1.1.9): http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.9.owl#
DAML: http://mged.sourceforge.net/ontologies/MGEDOntology.daml#
DAML (previous version 1.1.9): http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.9.daml#
DAML (previous version 1.1.8): http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.8.daml#
RDFS: The RDFS file was found to be missing things and has been retired until a complete copy of the daml version is generated.
definition:: Procedures used during treatment.
properties:
definition:: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).
properties:
definition:: One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition.
properties:
definition:: MAGE package that describes the array layout and design. The array may be physical or virtual.
properties:
definition:: An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
properties:
definition:: MAGE package for describing the process by which arrays were manufactured.
properties:
definition:: The atmospheric conditions used to culture or grow an organism.
properties:
definition:: An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
properties:
definition:: MAGE package for contacts including organizations and people.
properties:
definition:: Rating of containment system for the protection of organisms from infectious agents.
properties:
definition:: Refers to the bedding material present in an animals housing.
properties:
definition:: A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
properties:
definition:: A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
properties:
definition:: BioAssayData refers to the data files including images generated from one or more BioAssays.
properties:
definition:: A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
properties:
definition:: MAGE package for BioAssayData.
properties:
definition:: MAGE package for bioassay.
properties:
definition:: Description of the processing state of the biomaterial for use in the microarray hybridization.
properties:
definition:: General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
properties:
definition:: Properties of the biomaterial before treated in any manner for the purposes of the experiment.
properties:
definition:: Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
properties:
definition:: A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
properties:
definition:: BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.
properties:
definition:: The BioSource after any treatment.
properties:
definition:: Used to tell when the BioSample is an extract or not.
properties:
definition:: A representation of a DNA, RNA, or protein sequence.
properties:
definition:: MAGE package for biological sequences (biosequence).
properties:
definition:: Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus).
properties:
definition:: The BioSource is the original source material before any treatment events.
properties:
definition:: The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
properties:
definition:: The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources.
properties:
definition:: Factors that relate to properties of the biomaterial, its treatment, or its growth.
properties:
definition:: A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
properties:
definition:: Physical properties of the BioMaterial e. g. mass or height
properties:
definition:: class to hold instances used as the filler for the property has_cancer_site
properties:
definition:: The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
properties:
definition:: Database of cell line information.
properties:
definition:: CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.
properties:
definition:: Database of cell type information.
properties:
definition:: A structure within a cell, such as an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer).
properties:
definition:: A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
properties:
definition:: An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogenetic and microscopic techniques such as FISH.
properties:
definition:: An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.
properties:
definition:: The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
properties:
definition:: The current clinical treatment(s) of the patient from which the biosource is derived.
properties:
definition:: Database of clinical treatment information
properties:
definition:: Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
properties:
definition:: A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
properties:
definition:: Database of compound information.
properties:
definition:: Units used for concentration measurements.
properties:
definition:: Concentration units not specified in MAGE.
properties:
definition:: Organizations or individuals that may be contacted.
properties:
definition:: Controlled terms for descriptors for the type of control design element.
properties:
definition:: a plant variety obtained in agriculture in horticulture
properties:
definition:: The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
properties:
definition:: Primitive data types found in computing languages such as float, boolean, etc.
properties:
definition:: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
properties:
definition:: Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
properties:
definition:: Defects associated with features or zones such as those that are missing or moved.
properties:
definition:: Method used to deliver a compound for treatment.
properties:
definition:: Class to hold deprecated instances and classes.
properties:

Ontology Working Group

Ontology Container Information

Note that this page now reflects the latest version 1.3.1.1. The previous verion (1.2.0) displayed is still available as an OWL file (see link below)

Deprecated Biosequence terms

Notes and edits to MO 1.3

Notes and edits to MO 1.2

Notes and edits to MO 1.1.7/8/9

Ontology terms under review

Alternate views of the MGED Ontology

Files

Classes

Properties

Individuals

class Action

class Age

class Allele

class ArrayDesignPackage

class ArrayGroup

class ArrayPackage

class Atmosphere

class AtomicAction

class AuditAndSecurityPackage

class BarrierFacility

class Bedding

class BibliographicReference

class BioAssay

class BioAssayData

class BioAssayDataCluster

class BioAssayDataPackage

class BioAssayPackage

class BioMaterial

class BioMaterialCharacteristicCategory

class BioMaterialCharacteristics

class BioMaterialPackage

class BioMaterialPurity

class BioMolecularAnnotation

class BioSample

class BioSampleType

class BioSequence

class BioSequencePackage

class BioSequenceType

class BioSource

class BioSourceProvider

class BioSourceType

class BiologicalFactorCategory

class BiologicalProperty

class Biometrics

class CancerSite

class CellLine

class CellLineDatabase

class CellType

class CellTypeDatabase

class CellularComponent

class CellularComponentDatabase

class ChromosomalAberration

class ChromosomalAberrationClassification

class ClinicalHistory

class ClinicalTreatment

class ClinicalTreatmentDatabase

class ComplexAction

class Compound

class CompoundDatabase

class ConcentrationUnit

class ConcentrationUnitOther

class Contact

class ControlType

class Cultivar

class DataTransformationProtocolType

class DataType

class Database

class DatabaseEntryType

class DefectType

class DeliveryMethod

class DeprecatedTerms