Ontology Container Information

This site has been moved to http://mged.sourceforge.net/ontologies/MGEDontology.php for better management and integration with the MAGE effort. Any additions or changes will only be made at the new site. - Nov. 8, 2002.

Namespaces used

1

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

2

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

Classes

Age #1 Allele #1 Assay #2 Atmosphere #1 BarrierFacility #1 Bedding #1 BehavioralStimulus #1 BibliographicReference #1 BiologicalFactor #3 BiomaterialDescription #1 BiomaterialManipulation #1 BiomaterialMeasurement #1 BiomaterialPreparation #1 BiomaterialState #1 Biosample #1 Biosource #1 BiosourceOntologyEntry #1 BiosourceProperty #1 BiosourceProvider #1 CellLine #1 CellType #1 ClinicTreatmentHistory #1 ClinicalHistory #1 ClinicalInformation #1 Compound #1 CompoundBasedTreatment #1 ConcentrationUnit #1 Contact #1 ContaminantOrganism #1 CurrentDiseaseHistory #1 DatabaseEntry #1 DensityRange #1 DevelopmentalStage #1 DiseaseState #1 DistanceUnit #1 EnvironmentalHistory #1 FamilyHistory #1 Gender #1 Gene #1 Generations #1 GeneticModification #1 GeneticVariation #1 Genotype #1 GrowthCondition #1 Haplotype #1 Hardware #1 HardwareVariation #3 Histology #2 HistoryFactor #3 Host #1 Humidity #1 Individual #1 IndividualGeneticCharacterstics #1 Infection #1 LabeledExtract #1 Light #1 MGEDontology #3 MassUnit #1 Measurement #1 Medium #1 MethodologicalFactor #3 Modification #1 NormalizationDesign #3 Nutrients #1 OILED_DATATYPE #3 OntologyEntry #1 OperatorVariation #2 Organism #1 OrganismPart #1 Organization #1 PastMedicalHistory #1 PathogenTests #1 Person #1 PhysicalCharacteristics #2 Preservation #1 Protocol #1 ProtocolVariation #3 QualityControlDesign #3 QuantityUnit #1 ReplicateDesign #3 Resource #1 Sex #1 Software #1 SoftwareVariation #3 SomaticModification #1 Starvation #1 StrainOrLine #1 Study #3 StudyDesign #3 StudyFactor #3 TargetedCellType #1 Temperature #1 TemperatureUnit #1 TimeUnit #1 Treatment #1 URI #1 Unit #1 User #1 VolumeUnit #1 Water #1

Properties

Individuals

class Age #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting.

type:

primitive

superclasses:

BiosourceProperty #1

constraints:

restriction initial_time_point #1 has-class one-of (planting #1 coitus #1 beginning_of_stage #1 birth #1)
restriction has_measurement #1 has-class Measurement #1

used in properties:

initial_time_point #1

class Allele #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

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.

type:

primitive

superclasses:

IndividualGeneticCharacterstics #1

class Assay #2

namespace:

file:/Applications/OilEd3.4 Folder/ontologies/MGEDontology.daml#

documentation:

An assay is a single hybridization of one or more labelled extracts to an array.

type:

primitive

superclasses:

MGEDontology #3

used in classes:

Study #3
StudyDesign #3
StudyFactor #3

class Atmosphere #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The gases and their concentrations used during culture.

type:

primitive

superclasses:

GrowthCondition #1

class BarrierFacility #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The mechanism used to isolate the organism (e.g. keep mice free from infections).

type:

primitive

superclasses:

EnvironmentalHistory #1

constraints:

restriction description #1 has-class thing
restriction rating #1 has-class thing

class Bedding #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

This is a rodent thing. Will need to get a definition and see if it applies more generally to other organisms.

type:

primitive

superclasses:

EnvironmentalHistory #1

class BehavioralStimulus #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)

type:

primitive

superclasses:

Treatment #1

class BibliographicReference #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

A bibliographic reference is a published citation in a journal or book.

type:

primitive

superclasses:

Resource #1

constraints:

restriction year #1 has-class thing
restriction editor #1 has-class thing
restriction publisher #1 has-class thing
restriction publication #1 has-class thing
restriction authors #1 has-class thing
restriction title #1 has-class thing
restriction has_URI #1 has-class URI #1
restriction pages #1 has-class thing
restriction issue #1 has-class thing
restriction volume #1 has-class thing

used in classes:

Protocol #1
Study #3

used in properties:

issue #1
pages #1
volume #1

class BiologicalFactor #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

Factors that relate to properties of the biomaterial, its treatment, or its growth.

type:

primitive

superclasses:

StudyFactor #3

constraints:

restriction has_treatment #1 has-class Treatment #1
restriction has_biosource_ontology_entry #2 has-class BiosourceOntologyEntry #1

class BiomaterialDescription #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.

type:

primitive

superclasses:

MGEDontology #3

known subclasses:

BiomaterialManipulation #1
BiomaterialState #1
BiosourceProperty #1

used in classes:

BiomaterialManipulation #1
BiomaterialState #1
BiosourceProperty #1

class BiomaterialManipulation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Description of how the biomaterial has been manipulated including external influences such as environment, experimental treatment, and labeling.

type:

primitive

superclasses:

BiomaterialDescription #1

known subclasses:

BiomaterialPreparation #1
EnvironmentalHistory #1
Treatment #1

used in classes:

BiomaterialPreparation #1
BiomaterialState #1
EnvironmentalHistory #1
Treatment #1

class BiomaterialMeasurement #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Measurements that relate only to any biomaterial quantifiable, not for compound or general measurement

type:

primitive

superclasses:

Measurement #1

class BiomaterialPreparation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Description of how labeled biomaterial was prepared including harvesting, nucleic acid extraction, and labeling.

type:

primitive

superclasses:

BiomaterialManipulation #1

constraints:

restriction has_time_of_day #1 has-class Measurement #1
restriction was_prepared_by #1 has-class User #1
restriction pathological_staging #1 has-class one-of (postmortem #1 premortem #1)
restriction has_protocol #1 has-class Protocol #1
restriction biomaterial_amount #1 has-class Measurement #1
restriction biomaterial_purity #1 has-class OILED_DATATYPE #3

used in classes:

LabeledExtract #1

class BiomaterialState #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Description of the processing state of the biomaterial for use in the microarray hybridization.

type:

primitive

superclasses:

BiomaterialDescription #1

constraints:

restriction has_been_manipulated_by #1 has-class BiomaterialManipulation #1

known subclasses:

Biosample #1
Biosource #1
LabeledExtract #1

used in classes:

Biosample #1
Biosource #1
LabeledExtract #1

class Biosample #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The biosource after any treatment.

type:

primitive

superclasses:

BiomaterialState #1

constraints:

restriction has_been_manipulated_by #1 has-class Treatment #1

class Biosource #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The primary source of the nucleic acid used to generate labelled material for the microarray experiment.

type:

primitive

superclasses:

BiomaterialState #1

constraints:

restriction has_been_manipulated_by #1 has-class EnvironmentalHistory #1

class BiosourceOntologyEntry #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Controlled vocabulary or ontology that can be referred to in order to describe a biosource property.

type:

primitive

superclasses:

BiosourceProperty #1
OntologyEntry #1

constraints:

restriction ID #1 has-class thing
restriction description #1 has-class thing
restriction value #1 has-class thing
restriction has_database_entry #1 has-class DatabaseEntry #1

known subclasses:

CellLine #1
CellType #1
ClinicalInformation #1
DevelopmentalStage #1
DiseaseState #1
GeneticVariation #1
IndividualGeneticCharacterstics #1
Organism #1
OrganismPart #1
PhysicalCharacteristics #2
StrainOrLine #1
TargetedCellType #1

used in classes:

BiologicalFactor #3
CellLine #1
CellType #1
ClinicalInformation #1
DevelopmentalStage #1
DiseaseState #1
GeneticVariation #1
IndividualGeneticCharacterstics #1
Organism #1
OrganismPart #1
PhysicalCharacteristics #2
StrainOrLine #1
TargetedCellType #1

class BiosourceProperty #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Properties of the biomaterial before treated in any manner for the purposes of the experiment.

type:

primitive

superclasses:

BiomaterialDescription #1

constraints:

restriction is_user_defined #1 has-class User #1

known subclasses:

Age #1
BiosourceOntologyEntry #1
BiosourceProvider #1
Individual #1
Sex #1

used in classes:

Age #1
BiosourceOntologyEntry #1
BiosourceProvider #1
Individual #1
Sex #1

class BiosourceProvider #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The resource (e.g, company, hospital, geographical location) used to obtain or purchase the biomaterial.

type:

primitive

superclasses:

BiosourceProperty #1

constraints:

restriction has_donor #1 has-class Organization #1
restriction has_owner #1 has-class Person #1
restriction biosource_type #1 has-class one-of (blood_sample #1 paraffin_section #1 frozen_section #1 biopsy #1)

used in properties:

biosource_type #1

class CellLine #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The identifier for the immortalized cell line if one was used to derive the biomaterial.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in individuals:

CABRI #1

class CellType #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Cell type, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, eg of instance, epithelial, glial etc.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

class ClinicTreatmentHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The treatment history of the disease afflicting the patient from which the biosource is derived.

type:

primitive

superclasses:

ClinicalHistory #1

class ClinicalHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism's (i.e., the patient's) medical record as bacground information relevant to the experiment.

type:

primitive

superclasses:

EnvironmentalHistory #1

constraints:

restriction has_clinical_information #1 has-class ClinicalInformation #1
restriction has_lab_value #1 has-class Measurement #1

known subclasses:

ClinicTreatmentHistory #1
CurrentDiseaseHistory #1
PastMedicalHistory #1

used in classes:

ClinicTreatmentHistory #1
CurrentDiseaseHistory #1
PastMedicalHistory #1

class ClinicalInformation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Clinical information distinct from the disease state that can be referred to from an established controlled vocabulary or ontology. An example might be a test performed and/or finding.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in classes:

ClinicalHistory #1

used in individuals:

LOINC #3

class Compound #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

A drug, solvent, chemical, etc., that can be measured.

type:

primitive

superclasses:

OntologyEntry #1

constraints:

restriction is_solvent #1 has-class one-of (no #1 yes #1)

used in classes:

CompoundBasedTreatment #1
Nutrients #1
Water #1

used in individuals:

CASRegistryNumber #1
IUPAC #1

class CompoundBasedTreatment #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The treatment is effected by a defined chemical, biological, or physical agent or compound.

type:

primitive

superclasses:

Treatment #1

constraints:

restriction has_vehicle #1 has-class Compound #1
restriction treatment_application #1 has-class one-of (in_vitro #1 in_situ #1 in_vivo #1)
restriction has_protocol #1 has-class Protocol #1
restriction has_compound_measurement #1 has-class Measurement #1
restriction has_compound #1 has-class Compound #1
restriction has_delivery_method #1 has-class one-of (ad libitum #1 feeding #1 intramuscular #1 intraperitoneal #1 intravenous #1 oral_gavage #1 subcutaneous #1)

class ConcentrationUnit #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Units used for concentration measurements.

type:

primitive

superclasses:

Unit #1

used in individuals:

M #1
fM #1
g/l #1
mM #1
mg/ml #1
ml/l #1
pM #1
percent_vol/vol #1
percent_weight/vol #1
percent_weight/weight #1
uM #1

class Contact #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Organizations or individuals that may be contacted.

type:

primitive

superclasses:

Resource #1

constraints:

restriction email #1 has-class thing
restriction address #1 has-class thing
restriction has_URI #1 has-class URI #1
restriction phone #1 has-class thing
restriction toll_free_phone #1 has-class thing
restriction fax #1 has-class thing

known subclasses:

Organization #1
Person #1

used in classes:

Hardware #1
Organization #1
Person #1
Study #3

class ContaminantOrganism #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Organisms present that were not planned as part of the study (e.g., mycoplasma).

type:

primitive

superclasses:

Treatment #1

constraints:

restriction is_decontaminated_by #1 has-class Protocol #1
restriction is_contaminated_by #1 has-class Organism #1

used in properties:

is_decontaminated_by #1

class CurrentDiseaseHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The current course of the disease afflicting the patient from the biosource is deived.

type:

primitive

superclasses:

ClinicalHistory #1

class DatabaseEntry #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Reference to a URI.

type:

primitive

superclasses:

Resource #1

constraints:

restriction accession #1 has-class thing
restriction accession_version #1 has-class thing
restriction has_URI #1 has-class URI #1

used in classes:

BiosourceOntologyEntry #1
Gene #1
OntologyEntry #1

used in individuals:

CABRI_linenamesahc #1
CBIL_anat_id #1
ChemID #1
FlyBase_cv_id #1
GALENCommonReferenceModel #3
ICD-9-CM_2001 #3
JAX_mouse_strains #1
LOINCDatabase #3
MAD_stage #1
MESH2002 #3
MTBDatabase #3
NCBI_taxon_id #1
TDMSPathologyCodeTables #3
WebRENI #3

class DensityRange #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The concentration range of the organism.

type:

primitive

superclasses:

GrowthCondition #1

class DevelopmentalStage #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The developmental stage of the organism's life cycle during which the biomaterial was extracted.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in individuals:

MouseAnatomicalDictionary #1

class DiseaseState #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in individuals:

GALEN #3
ICD-9-CM #3
MESH #3
MouseTumorBiology #3
NTPCodeTables #3
RENI #3
SNOMED #3
UMLS #3

class DistanceUnit #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Units used for distance measurements.

type:

primitive

superclasses:

Unit #1

used in individuals:

A #1
cm #1
m #1
mm #1
nm #1
um #1

class EnvironmentalHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

A description of the conditions the organism has been exposed to that are not one of the variables under study.

type:

primitive

superclasses:

BiomaterialManipulation #1

known subclasses:

BarrierFacility #1
Bedding #1
ClinicalHistory #1
FamilyHistory #1
Nutrients #1
PathogenTests #1

used in classes:

BarrierFacility #1
Bedding #1
Biosource #1
ClinicalHistory #1
FamilyHistory #1
Nutrients #1
PathogenTests #1

class FamilyHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Relevant aspects of genetic preconditions or family members clinical history.

type:

primitive

superclasses:

EnvironmentalHistory #1

class Gender #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender.

type:

primitive

superclasses:

Sex #1

used in individuals:

female #1
hermaphrodite #1
male #1
mixed_sex #1
unknown_sex #1

class Gene #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Genetic unit composed of DNA.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction has_database_entry #1 has-class DatabaseEntry #1

used in classes:

GeneticModification #1

class Generations #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The number of cell divisions if the organism or organism part that is cultured is unicellular otherwise the number of breedings.

type:

primitive

superclasses:

GrowthCondition #1

class GeneticModification #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism has had genes removed, added, or rearranged.

type:

primitive

superclasses:

Modification #1

constraints:

restriction gene_modified #1 has-class Gene #1

class GeneticVariation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

class Genotype #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The total sum of the genetic information of an organism that is known and relevant to the experiment being performed.

type:

primitive

superclasses:

IndividualGeneticCharacterstics #1

class GrowthCondition #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.

type:

primitive

superclasses:

Treatment #1

constraints:

restriction has_measurement #1 has-class Measurement #1

known subclasses:

Atmosphere #1
DensityRange #1
Generations #1
Host #1
Humidity #1
Light #1
Medium #1
Nutrients #1
Temperature #1
Water #1

used in classes:

Atmosphere #1
DensityRange #1
Generations #1
Host #1
Humidity #1
Light #1
Medium #1
Nutrients #1
Temperature #1
Water #1

class Haplotype #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.

type:

primitive

superclasses:

IndividualGeneticCharacterstics #1

class Hardware #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The machine or instrument used.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction make #1 has-class thing
restriction has_manufacturer #1 has-class Contact #1
restriction model #1 has-class thing

used in classes:

Protocol #1

used in properties:

make #1
model #1

class HardwareVariation #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.

type:

primitive

superclasses:

MethodologicalFactor #3

class Histology #2

namespace:

file:/Applications/OilEd3.4 Folder/ontologies/MGEDontology.daml#

documentation:

Microscopic morphology of tissues.

type:

primitive

superclasses:

OrganismPart #1

class HistoryFactor #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).

type:

primitive

superclasses:

StudyFactor #3

class Host #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).

type:

primitive

superclasses:

GrowthCondition #1

constraints:

restriction has_host #1 has-class Organism #1
restriction has_host_part #1 has-class OrganismPart #1

used in properties:

has_host #1
has_host_part #1

class Humidity #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The humidity that the biosource is exposed to.

type:

primitive

superclasses:

GrowthCondition #1

class Individual #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Identifier or name of the individual organism from which the biomaterial was derived.

type:

primitive

superclasses:

BiosourceProperty #1

constraints:

restriction ID #1 has-class thing

class IndividualGeneticCharacterstics #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

known subclasses:

Allele #1
Genotype #1
Haplotype #1

used in classes:

Allele #1
Genotype #1
Haplotype #1

class Infection #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism (or organism part) has been exposed to a virus or pathogen.

type:

primitive

superclasses:

Treatment #1

constraints:

restriction infected_by #1 has-class Organism #1

class LabeledExtract #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The biosample after labeling for detection of the nucleic acids.

type:

primitive

superclasses:

BiomaterialState #1

constraints:

restriction has_been_manipulated_by #1 has-class BiomaterialPreparation #1

class Light #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.

type:

primitive

superclasses:

GrowthCondition #1

class MGEDontology #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

An ontology developed by the Microarray Gene Expression Data (MGED) group to describe the different parts of a microarray experiment.

type:

primitive

constraints:

restriction ID #1 has-class thing

known subclasses:

Assay #2
BiomaterialDescription #1
Gene #1
Hardware #1
Measurement #1
Protocol #1
Resource #1
Software #1
Study #3
StudyDesign #3
StudyFactor #3
URI #1
Unit #1

used in classes:

Assay #2
BiomaterialDescription #1
Gene #1
Hardware #1
Measurement #1
Protocol #1
Resource #1
Software #1
Study #3
StudyDesign #3
StudyFactor #3
URI #1
Unit #1

class MassUnit #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Units used for mass measurements.

type:

primitive

superclasses:

Unit #1

used in individuals:

fg #1
g #1
kg #1
mg #1
ng #1
pg #1
ug #1

class Measurement #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Measured values and units.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction value #1 has-class thing
restriction has_units #1 has-class Unit #1
restriction measurement_type #1 has-class one-of (change #1 absolute #1)

known subclasses:

BiomaterialMeasurement #1

used in classes:

Age #1
BiomaterialMeasurement #1
BiomaterialPreparation #1
ClinicalHistory #1
CompoundBasedTreatment #1
GrowthCondition #1

used in properties:

measurement_type #1

class Medium #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)

type:

primitive

superclasses:

GrowthCondition #1

constraints:

restriction matrix_used #1 has-class one-of (liquid #1 agar #1 semisolid #1 soil #1)

class MethodologicalFactor #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.

type:

primitive

superclasses:

StudyFactor #3

known subclasses:

HardwareVariation #3
OperatorVariation #2
ProtocolVariation #3
SoftwareVariation #3

used in classes:

HardwareVariation #3
OperatorVariation #2
ProtocolVariation #3
SoftwareVariation #3

class Modification #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

A treatment that involves adding, removing, or rearranging in the biosource.

type:

primitive

superclasses:

Treatment #1

constraints:

restriction modification_type #1 has-class one-of (rearrangement #1 removal #1 addition #1)

known subclasses:

GeneticModification #1
SomaticModification #1

used in classes:

GeneticModification #1
SomaticModification #1

class NormalizationDesign #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

Groups of assays whose data have been processed to be diretly comparable.

type:

primitive

superclasses:

StudyDesign #3

class Nutrients #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

type:

primitive

superclasses:

EnvironmentalHistory #1
GrowthCondition #1

constraints:

restriction nutrient_component #1 has-class Compound #1

used in classes:

Starvation #1

class OILED_DATATYPE #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

type:

primitive

used in classes:

BiomaterialPreparation #1

class OntologyEntry #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Controlled vocabulary or ontology that can be referred to.

type:

primitive

superclasses:

Resource #1

constraints:

restriction ID #1 has-class thing
restriction description #1 has-class thing
restriction value #1 has-class thing
restriction has_database_entry #1 has-class DatabaseEntry #1

known subclasses:

BiosourceOntologyEntry #1
Compound #1

used in classes:

BiosourceOntologyEntry #1
Compound #1

class OperatorVariation #2

namespace:

file:/Applications/OilEd3.4 Folder/ontologies/MGEDontology.daml#

documentation:

The effects of different investigators, laboratories, or organizations on experimental results are studied.

type:

primitive

superclasses:

MethodologicalFactor #3

class Organism #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The genus and species (and subspecies) of the organism from which the biomaterial is derived from.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in classes:

ContaminantOrganism #1
Host #1
Infection #1
PathogenTests #1

used in individuals:

NCBI_taxonomy #1

class OrganismPart #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The part of the organism's anatomy from which the biomaterial was derived.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

known subclasses:

Histology #2

used in classes:

Histology #2
Host #1
SomaticModification #1

used in individuals:

CBIL_CV #1
FlyBase #1
MouseAnatomicalDictionary #1

class Organization #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organization (e.g, company, hospital) to contact to obtain or purchase something.

type:

primitive

superclasses:

Contact #1

constraints:

restriction name #1 has-class thing
restriction has_parent_organization #3 has-class Organization #1

used in classes:

BiosourceProvider #1
Organization #1
Person #1

class PastMedicalHistory #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The past medical history of the patient that the biosource is derived from.

type:

primitive

superclasses:

ClinicalHistory #1

class PathogenTests #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Tests and results for pathogens infecting organism from which the biosource is derived

type:

primitive

superclasses:

one-of (SPF #1 non-SPF #1)
EnvironmentalHistory #1

constraints:

restriction result_summary #1 has-class one-of (negative #1 inconclusive #1 positive #1)
restriction tested_for #1 has-class Organism #1

class Person #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The individual to contact regarding something provided such as a biomaterial.

type:

primitive

superclasses:

Contact #1

constraints:

restriction mid_initials #1 has-class thing
restriction last_name #1 has-class thing
restriction has_affiliation #1 has-class Organization #1
restriction first_name #1 has-class thing

known subclasses:

User #1

used in classes:

BiosourceProvider #1
User #1

class PhysicalCharacteristics #2

namespace:

file:/Applications/OilEd3.4 Folder/ontologies/MGEDontology.daml#

documentation:

Phenotype and traits not including pathology and disease.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

class Preservation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Method and type of preserving the organism or biosource (i.e. keeping it in stasis).

type:

primitive

superclasses:

Treatment #1

constraints:

restriction has_protocol #1 has-class Protocol #1
restriction preservation_type #1 has-class one-of (seed_dormancy #1 frozen_storage #1)

class Protocol #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Documentation of the set of steps taken in a procedure.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction has_software #1 has-class Software #1
restriction has_citation #1 has-class BibliographicReference #1
restriction name #1 has-class thing
restriction description #1 has-class thing
restriction has_hardware #1 has-class Hardware #1

used in classes:

BiomaterialPreparation #1
CompoundBasedTreatment #1
ContaminantOrganism #1
Preservation #1
Treatment #1
Water #1

class ProtocolVariation #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The effects of different protocols or changes in protocols on experimental results are studied.

type:

primitive

superclasses:

MethodologicalFactor #3

class QualityControlDesign #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

Group of assays that are related as part of quality control.

type:

primitive

superclasses:

StudyDesign #3

class QuantityUnit #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Units used for quantity measurements.

type:

primitive

superclasses:

Unit #1

used in individuals:

amol #1
fmol #1
mol #1
molecules #1
nmol #1
pmol #1
umol #1

class ReplicateDesign #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

Groups of assays that represent biological or technical replicates.

type:

primitive

superclasses:

StudyDesign #3

class Resource #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Something or someone you get stuff from. Can be a web site, organization, or individual. Stuff can be information or biomaterial.

type:

primitive

superclasses:

MGEDontology #3

known subclasses:

BibliographicReference #1
Contact #1
DatabaseEntry #1
OntologyEntry #1

used in classes:

BibliographicReference #1
Contact #1
DatabaseEntry #1
OntologyEntry #1

class Sex #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.

type:

primitive

superclasses:

BiosourceProperty #1

known subclasses:

Gender #1

used in classes:

Gender #1

used in individuals:

F+ #1
F- #1
Hfr #1
mating_type_a #1
mating_type_alpha #1
mixed_sex #1
unknown_sex #1

class Software #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The software application used.

type:

primitive

superclasses:

MGEDontology #3

used in classes:

Protocol #1

class SoftwareVariation #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The effects of different software, software packages, or spftware versions on experimental results are studied.

type:

primitive

superclasses:

MethodologicalFactor #3

class SomaticModification #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism has had non-genetic parts removed, added, or rearranged.

type:

primitive

superclasses:

Modification #1

constraints:

restriction has_part_modified #1 has-class OrganismPart #1

class Starvation #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

The organism (or organism part) has been deprived of nutrients.

type:

primitive

superclasses:

Treatment #1

constraints:

restriction starved_of #1 has-class Nutrients #1

class StrainOrLine #1

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.rdfs#

documentation:

Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings.

type:

primitive

superclasses:

BiosourceOntologyEntry #1

used in individuals:

IntlComStdGenNomMice_Strains #1

class Study #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The complete set of assays and their descriptions performed as a study for a common purpose, In general, a study will be equivalent to a publication.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction has_study_design #2 has-class StudyDesign #3
restriction has_citation #1 has-class BibliographicReference #1
restriction has_URI #1 has-class URI #1
restriction number_of_assays #2 has-class thing
restriction has_submitter #2 has-class Contact #1
restriction has_assay #2 has-class Assay #2

class StudyDesign #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation:

The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.

type:

primitive

superclasses:

MGEDontology #3

constraints:

restriction has_study_factor #2 has-class StudyFactor #3
restriction description #1 has-class thing
restriction has_assay #2 has-class Assay #2

known subclasses:

NormalizationDesign #3
QualityControlDesign #3
ReplicateDesign #3

used in classes:

NormalizationDesign #3
QualityControlDesign #3
ReplicateDesign #3
Study #3

class StudyFactor #3

namespace:

http://www.cbil.upenn.edu/Ontology/MGEDontology.daml#

documentation: