Ontology Container Information

Namespaces used

default

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

1

http://www.cbil.upenn.edu/Ontology/biomaterial14.daml#

A picture from OILed of the class tree (coutesy John Matese)

Classes

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

Properties

Individuals

class Age

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

constraints:

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

used in properties:

initial_time_point

class Allele

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class Atmosphere

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The gases and their concentrations used during culture.

type:

primitive

superclasses:

GrowthCondition

class BarrierFacility

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

restriction description has-class thing
restriction rating has-class thing

class Bedding

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class BehavioralStimulus

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class BibliographicReference

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Resource

constraints:

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

used in classes:

Protocol

used in properties:

issue
pages
volume

class BiomaterialDescription

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

MGEDontology #1

known subclasses:

BiomaterialManipulation
BiomaterialState
BiosourceProperty

used in classes:

BiomaterialManipulation
BiomaterialState
BiosourceProperty

class BiomaterialManipulation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiomaterialDescription

known subclasses:

BiomaterialPreparation
EnvironmentalHistory
Treatment

used in classes:

BiomaterialPreparation
BiomaterialState
EnvironmentalHistory
Treatment

class BiomaterialMeasurement

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Measurement

class BiomaterialPreparation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiomaterialManipulation

constraints:

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

used in classes:

LabeledExtract

class BiomaterialState

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiomaterialDescription

constraints:

restriction has_been_manipulated_by has-class BiomaterialManipulation

known subclasses:

Biosample
Biosource
LabeledExtract

used in classes:

Biosample
Biosource
LabeledExtract

class Biosample

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The biosource after any treatment.

type:

primitive

superclasses:

BiomaterialState

constraints:

restriction has_been_manipulated_by has-class Treatment

class Biosource

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiomaterialState

constraints:

restriction has_been_manipulated_by has-class EnvironmentalHistory

class BiosourceOntologyEntry

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceProperty
OntologyEntry

constraints:

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

known subclasses:

CellLine
CellType
ClinicalInformation
DevelopmentalStage
DiseaseState
GeneticVariation
IndividualGeneticCharacterstics
Organism
OrganismPart
StrainOrLine
TargetedCellType

used in classes:

CellLine
CellType
ClinicalInformation
DevelopmentalStage
DiseaseState
GeneticVariation
IndividualGeneticCharacterstics
Organism
OrganismPart
StrainOrLine
TargetedCellType

class BiosourceProperty

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiomaterialDescription

constraints:

restriction is_user_defined has-class User

known subclasses:

Age
BiosourceOntologyEntry
BiosourceProvider
Individual
Sex

used in classes:

Age
BiosourceOntologyEntry
BiosourceProvider
Individual
Sex

class BiosourceProvider

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceProperty

constraints:

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

used in properties:

biosource_type

class CellLine

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceOntologyEntry

used in individuals:

CABRI

class CellType

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class ClinicTreatmentHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class ClinicalHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

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

known subclasses:

ClinicTreatmentHistory
CurrentDiseaseHistory
PastMedicalHistory

used in classes:

ClinicTreatmentHistory
CurrentDiseaseHistory
PastMedicalHistory

class ClinicalInformation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

used in classes:

ClinicalHistory

used in individuals:

LOINC #1

class Compound

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

OntologyEntry

constraints:

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

used in classes:

CompoundBasedTreatment
Nutrients
Water

used in individuals:

CASRegistryNumber
IUPAC

class CompoundBasedTreatment

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment
one-of (intraperitoneal)

constraints:

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

class ConcentrationUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for concentration measurements.

type:

primitive

superclasses:

Unit

used in individuals:

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

class Contact

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Organizations or individuals that may be contacted.

type:

primitive

superclasses:

Resource

constraints:

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

known subclasses:

Organization
Person

used in classes:

Hardware
Organization
Person

class ContaminantOrganism

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

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

used in properties:

is_decontaminated_by

class CurrentDiseaseHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class DatabaseEntry

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Reference to a URI.

type:

primitive

superclasses:

Resource

constraints:

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

used in classes:

BiosourceOntologyEntry
Gene
OntologyEntry

used in individuals:

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

class DensityRange

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The concentration range of the organism.

type:

primitive

superclasses:

GrowthCondition

class DevelopmentalStage

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceOntologyEntry

used in individuals:

MouseAnatomicalDictionary

class DiseaseState

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

used in individuals:

GALEN #1
ICD-9-CM #1
MESH #1
MouseTumorBiology #1
NTPCodeTables #1
RENI #1
SNOMED #1
UMLS #1

class DistanceUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for distance measurements.

type:

primitive

superclasses:

Unit

used in individuals:

A
cm
m
mm
nm
um

class EnvironmentalHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

known subclasses:

BarrierFacility
Bedding
ClinicalHistory
FamilyHistory
Nutrients
PathogenTests

used in classes:

BarrierFacility
Bedding
Biosource
ClinicalHistory
FamilyHistory
Nutrients
PathogenTests

class FamilyHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Relevant aspects of genetic preconditions or family members clinical history.

type:

primitive

superclasses:

EnvironmentalHistory

class Gender

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

used in individuals:

female
hermaphrodite
male
mixed_sex
unknown_sex

class Gene

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Genetic unit composed of DNA.

type:

primitive

superclasses:

MGEDontology #1

constraints:

restriction has_database_entry has-class DatabaseEntry

used in classes:

GeneticModification

class Generations

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class GeneticModification

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Modification

constraints:

restriction gene_modified has-class Gene

class GeneticVariation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class Genotype

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class GrowthCondition

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

constraints:

restriction has_measurement has-class Measurement

known subclasses:

Atmosphere
DensityRange
Generations
Host
Humidity
Light
Medium
Nutrients
Temperature
Water

used in classes:

Atmosphere
DensityRange
Generations
Host
Humidity
Light
Medium
Nutrients
Temperature
Water

class Haplotype

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

class Hardware

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The machine or instrument used.

type:

primitive

superclasses:

MGEDontology #1

constraints:

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

used in classes:

Protocol

used in properties:

make
model

class Host

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

constraints:

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

used in properties:

has_host
has_host_part

class Humidity

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The humidity that the biosource is exposed to.

type:

primitive

superclasses:

GrowthCondition

class Individual

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceProperty

constraints:

restriction ID has-class thing

class IndividualGeneticCharacterstics

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

known subclasses:

Allele
Genotype
Haplotype

used in classes:

Allele
Genotype
Haplotype

class Infection

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

restriction infected_by has-class Organism

class LabeledExtract

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The biosample after labeling for detection of the nucleic acids.

type:

primitive

superclasses:

BiomaterialState

constraints:

restriction has_been_manipulated_by has-class BiomaterialPreparation

class Light

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

GrowthCondition

class MGEDontology #1

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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 has-class thing

known subclasses:

BiomaterialDescription
Gene
Hardware
Measurement
Protocol
Resource
Software
URI
Unit

used in classes:

BiomaterialDescription
Gene
Hardware
Measurement
Protocol
Resource
Software
URI
Unit

class MassUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for mass measurements.

type:

primitive

superclasses:

Unit

used in individuals:

fg
g
kg
mg
ng
pg
ug

class Measurement

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Measured values and units.

type:

primitive

superclasses:

MGEDontology #1

constraints:

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

known subclasses:

BiomaterialMeasurement

used in classes:

Age
BiomaterialMeasurement
BiomaterialPreparation
ClinicalHistory
CompoundBasedTreatment
GrowthCondition

used in properties:

measurement_type

class Medium

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

GrowthCondition

constraints:

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

class Modification

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

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

known subclasses:

GeneticModification
SomaticModification

used in classes:

GeneticModification
SomaticModification

class Nutrients

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory
GrowthCondition

constraints:

restriction nutrient_component has-class Compound

used in classes:

Starvation

class OILED_DATATYPE #1

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.daml#

type:

primitive

used in classes:

BiomaterialPreparation

class OntologyEntry

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Controlled vocabulary or ontology that can be referred to.

type:

primitive

superclasses:

Resource

constraints:

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

known subclasses:

BiosourceOntologyEntry
Compound

used in classes:

BiosourceOntologyEntry
Compound

class Organism

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceOntologyEntry

used in classes:

ContaminantOrganism
Host
Infection
PathogenTests

used in individuals:

NCBI_taxonomy

class OrganismPart

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

BiosourceOntologyEntry

used in classes:

Host
SomaticModification

used in individuals:

CBIL_CV
FlyBase
MouseAnatomicalDictionary

class Organization

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Contact

constraints:

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

used in classes:

BiosourceProvider
Organization
Person

class PastMedicalHistory

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class PathogenTests

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

one-of (SPF non-SPF)
EnvironmentalHistory

constraints:

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

class Person

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Contact

constraints:

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

known subclasses:

User

used in classes:

BiosourceProvider
User

class Preservation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

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

class Protocol

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Documentation of the set of steps taken in a procedure.

type:

primitive

superclasses:

MGEDontology #1

constraints:

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

used in classes:

BiomaterialPreparation
CompoundBasedTreatment
ContaminantOrganism
Preservation
Treatment
Water

class QuantityUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for quantity measurements.

type:

primitive

superclasses:

Unit

used in individuals:

amol
fmol
mol
molecules
nmol
pmol
umol

class Resource

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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 #1

known subclasses:

BibliographicReference
Contact
DatabaseEntry
OntologyEntry

used in classes:

BibliographicReference
Contact
DatabaseEntry
OntologyEntry

class Sex

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

known subclasses:

Gender

used in classes:

Gender

used in individuals:

F+
F-
Hfr
mating_type_a
mating_type_alpha
mixed_sex
unknown_sex

class Software

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The software application used.

type:

primitive

superclasses:

MGEDontology #1

used in classes:

Protocol

class SomaticModification

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Modification

constraints:

restriction has_part_modified has-class OrganismPart

class Starvation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

restriction starved_of has-class Nutrients

class StrainOrLine

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.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

used in individuals:

IntlComStdGenNomMice_Strains

class TargetedCellType

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest.

type:

primitive

superclasses:

BiosourceOntologyEntry

used in individuals:

CBIL_CV
FlyBase
MouseAnatomicalDictionary

class Temperature

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The temperature that a biosource is exposed to.

type:

primitive

superclasses:

GrowthCondition

class TemperatureUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for temperature measurements.

type:

primitive

superclasses:

Unit

used in individuals:

degrees_C
degrees_F
degrees_K

class TimeUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for time measurements.

type:

primitive

superclasses:

Unit

used in individuals:

days
hours
minutes
months
ms
seconds
us
weeks
years

class Treatment

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

The manipulation of the biomaterial for the purposes of generating one of the variables under study.

type:

primitive

superclasses:

BiomaterialManipulation

constraints:

restriction has_protocol has-class Protocol

known subclasses:

BehavioralStimulus
CompoundBasedTreatment
ContaminantOrganism
GrowthCondition
Infection
Modification
Preservation
Starvation

used in classes:

BehavioralStimulus
Biosample
CompoundBasedTreatment
ContaminantOrganism
GrowthCondition
Infection
Modification
Preservation
Starvation

class URI

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Uniform Resource Identifier

type:

primitive

superclasses:

MGEDontology #1

used in classes:

BibliographicReference
Contact
DatabaseEntry

used in individuals:

chem.sis.nlm.nih.gov/chemidplus
flybase.bio.indiana.edu/.bin/cvreport.html?id=
ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2001/ #1
www.cabri.org/CABRI/home/guidelines/catalogue/CPCel linenamesahc.html
www.cbil.upenn.edu/servlet/allgenes-dev/servlet?page=anat&id=
www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
www.informatics.jax.org/mgihome/GXD/AD/
www.ita.fhg.de/reni/index.htm #1
www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=
www.nlm.nih.gov/mesh/filelist.html #1
www.opengalen.org/open/crm/crm.html #1
www.regenstrief.org/loinc/downloads.html #1

class Unit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units of measure.

type:

primitive

superclasses:

MGEDontology #1

known subclasses:

ConcentrationUnit
DistanceUnit
MassUnit
QuantityUnit
TemperatureUnit
TimeUnit
VolumeUnit

used in classes:

ConcentrationUnit
DistanceUnit
MassUnit
Measurement
QuantityUnit
TemperatureUnit
TimeUnit
VolumeUnit

class User

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

User defined term not present in external ontology or MGED list of biosource properties, like age sex etc

type:

primitive

superclasses:

Person

constraints:

restriction ID has-class thing

used in classes:

BiomaterialPreparation
BiosourceProperty

class VolumeUnit

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Units used for volume measurements.

type:

primitive

superclasses:

Unit

used in individuals:

cc
dl
fl
l
ml
nl
pl
ul

class Water

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

documentation:

Water consumed by or enveloping the organism that the biosource is derived from.

type:

primitive

superclasses:

GrowthCondition

constraints:

restriction has_treatment has-class Protocol
restriction has_additive has-class Compound

property ID

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BiosourceOntologyEntry
Individual
MGEDontology #1
OntologyEntry
User

property accession

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

properties:

functional

used in classes:

DatabaseEntry

property accession_version

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

properties:

functional

used in classes:

DatabaseEntry

property address

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Contact

property authors

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BibliographicReference

property biomaterial_amount

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BiomaterialPreparation

property biomaterial_purity

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BiomaterialPreparation

property biosource_type

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

domain:

BiosourceProvider

properties:

functional

used in classes:

BiosourceProvider

property description

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BarrierFacility
BiosourceOntologyEntry
OntologyEntry
Protocol

property editor

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

BibliographicReference

property email

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Contact

property fax

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Contact

property first_name

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Person

property gene_modified

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

GeneticModification

property has_URI

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

properties:

functional

used in classes:

BibliographicReference
Contact
DatabaseEntry

used in individuals:

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

property has_additive

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Water

property has_affiliation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Person

property has_been_manipulated_by

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

properties:

functional

used in classes:

BiomaterialState
Biosample
Biosource
LabeledExtract

property has_category

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

property has_citation

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

Protocol

property has_clinical_information

namespace:

http://www.cbil.upenn.edu/Ontology/biomaterial14.rdfs#

used in classes:

ClinicalHistory

property