Ontology Container Information

Title:

"An MGED Ontology for Biomaterial"

Creator:

Chris Stoeckert

Description:

Description of the sample (biomaterial) used in a microarray experiment.

Release:

"1.1"

Classes:

75

Slots:

70

Individuals:

98

Axioms:

0

Classes

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

Slots

Individuals

class Age

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:

slot-constraint has_measurement has-value Measurement
slot-constraint initial_time_point has-value one-of (beginning_of_stage planting)

used in slots:

initial_time_point

class Atmosphere

documentation:

The gases and their concentrations used during culture.

type:

primitive

superclasses:

CultureCondition

class BarrierFacility

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint description has-value top
slot-constraint rating has-value top

class Bedding

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

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

documentation:

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

type:

primitive

superclasses:

Resource

constraints:

slot-constraint editor has-value top
slot-constraint year has-value top
slot-constraint volume has-value top
slot-constraint issue has-value top
slot-constraint pages has-value top
slot-constraint has_URI has-value URI
slot-constraint title has-value top
slot-constraint authors has-value top
slot-constraint publication has-value top
slot-constraint publisher has-value top

used in classes:

Protocol

used in slots:

issue
pages
volume

class BiomaterialDescription

documentation:

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

type:

primitive

known subclasses:

BiomaterialManipulation
BiomaterialState
BiosourceProperty

used in classes:

BiomaterialManipulation
BiomaterialState
BiosourceProperty

class BiomaterialManipulation

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 BiomaterialPreparation

documentation:

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

type:

primitive

superclasses:

BiomaterialManipulation

constraints:

slot-constraint has_time_of_day has-value Measurement
slot-constraint has_protocol has-value Protocol
slot-constraint biomaterial_purity has-value range 100 0)
slot-constraint biomaterial_amount has-value Measurement
slot-constraint pathological_staging has-value one-of (postmortem premortem)

used in classes:

LabeledExtract

class BiomaterialState

documentation:

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

type:

primitive

superclasses:

BiomaterialDescription

constraints:

slot-constraint has_been_manipulated_by has-value BiomaterialManipulation

known subclasses:

Biosample
Biosource
LabeledExtract

used in classes:

Biosample
Biosource
LabeledExtract

class Biosample

documentation:

The biosource after any treatment.

type:

primitive

superclasses:

BiomaterialState

constraints:

slot-constraint has_been_manipulated_by has-value Treatment

class Biosource

documentation:

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

type:

primitive

superclasses:

BiomaterialState

constraints:

slot-constraint has_been_manipulated_by has-value EnvironmentalHistory

class BiosourceOntologyEntry

documentation:

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

type:

primitive

superclasses:

OntologyEntry
BiosourceProperty

constraints:

slot-constraint value has-value top
slot-constraint description has-value top
slot-constraint ID has-value top
slot-constraint has_database_entry has-value DatabaseEntry

known subclasses:

CellLine
ClinicalInformation
DevelopmentalStage
DiseaseState
GeneticVariation
IndividualGeneticCharacterstics
Organism
OrganismPart
StrainOrLine
TargetedCellType

used in classes:

CellLine
ClinicalInformation
DevelopmentalStage
DiseaseState
GeneticVariation
IndividualGeneticCharacterstics
Organism
OrganismPart
StrainOrLine
TargetedCellType

class BiosourceProperty

documentation:

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

type:

primitive

superclasses:

BiomaterialDescription

known subclasses:

Age
BiosourceOntologyEntry
BiosourceProvider
Individual
Sex

used in classes:

Age
BiosourceOntologyEntry
BiosourceProvider
Individual
Sex

class BiosourceProvider

documentation:

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

type:

primitive

superclasses:

BiosourceProperty

constraints:

slot-constraint has_owner has-value Person
slot-constraint has_donor has-value Organization
slot-constraint biosource_type has-value one-of (paraffin_section biopsy)

used in slots:

biosource_type

class CellLine

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 ClinicTreatmentHistory

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class ClinicalHistory

documentation:

The organism's (i.e., the patient's) medical record.

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint has_lab_values has-value Measurement
slot-constraint has_clinical_information has-value ClinicalInformation

known subclasses:

ClinicTreatmentHistory
CurrentDiseaseHistory
PastMedicalHistory

used in classes:

ClinicTreatmentHistory
CurrentDiseaseHistory
PastMedicalHistory

class ClinicalInformation

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

class Compound

documentation:

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

type:

primitive

superclasses:

OntologyEntry

constraints:

slot-constraint is_solvent has-value one-of (no yes)

used in classes:

CompoundBasedTreatment
Nutrients
Water

used in individuals:

CASRegistryNumber
IUPAC

class CompoundBasedTreatment

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

slot-constraint treatment_application has-value one-of (in_situ in_vivo in_vitro)
slot-constraint has_compound has-value Compound
slot-constraint has_compound_measurement has-value Measurement
slot-constraint has_protocol has-value Protocol

class ConcentrationUnit

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

documentation:

Organizations or individuals that may be contacted.

type:

primitive

superclasses:

Resource

constraints:

slot-constraint address has-value top
slot-constraint email has-value top
slot-constraint fax has-value top
slot-constraint toll_free_phone has-value top
slot-constraint phone has-value top
slot-constraint has_URI has-value URI

known subclasses:

Organization
Person

used in classes:

Hardware
Organization
Person

class ContaminantOrganism

documentation:

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

type:

primitive

superclasses:

CultureCondition

constraints:

slot-constraint is_decontaminated_by has-value Protocol
slot-constraint is_contaminated_by has-value Organism

used in slots:

is_decontaminated_by

class CultureCondition

documentation:

A description of the isolated environment used to grow organisms or parts of the organism.

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint has_measurement has-value Measurement

known subclasses:

Atmosphere
ContaminantOrganism
DensityRange
Generations
Host
Humidity
Light
Medium
Nutrients
Temperature

used in classes:

Atmosphere
ContaminantOrganism
DensityRange
Generations
Host
Humidity
Light
Medium
Nutrients
Temperature

class CurrentDiseaseHistory

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class DatabaseEntry

documentation:

Reference to a URI.

type:

primitive

superclasses:

Resource

constraints:

slot-constraint accession has-value top
slot-constraint has_URI has-value URI
slot-constraint accession_version has-value top

used in classes:

BiosourceOntologyEntry
Gene
OntologyEntry

used in individuals:

CABRI_linenamesahc
CBIL_anat_id
ChemID
FlyBase_cv_id
JAX_mouse_strains
MAD_stage
NCBI_taxon_id

class DensityRange

documentation:

The concentration range of the organism.

type:

primitive

superclasses:

CultureCondition

class DevelopmentalStage

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

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

class DistanceUnit

documentation:

Units used for distance measurements.

type:

primitive

superclasses:

Unit

used in individuals:

A
cm
m
mm
nm
um

class EnvironmentalHistory

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
CultureCondition
FamilyHistory
PathogenTests
Preservation
Water

used in classes:

BarrierFacility
Bedding
Biosource
ClinicalHistory
CultureCondition
FamilyHistory
PathogenTests
Preservation
Water

class FamilyHistory

documentation:

Relevant aspects of genetic preconditions or family members clinical history.

type:

primitive

superclasses:

EnvironmentalHistory

class Gene

documentation:

Genetic unit composed of DNA.

type:

primitive

constraints:

slot-constraint has_database_entry has-value DatabaseEntry

used in classes:

GeneticModification

class Generations

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:

CultureCondition

class GeneticModification

documentation:

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

type:

primitive

superclasses:

Modification

constraints:

slot-constraint gene_modified has-value Gene

class GeneticVariation

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 Hardware

documentation:

The machine or instrument used.

type:

primitive

constraints:

slot-constraint has_manufacturer has-value Contact
slot-constraint make has-value top
slot-constraint model has-value top

used in classes:

Protocol

used in slots:

make
model

class Host

documentation:

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

type:

primitive

superclasses:

CultureCondition

constraints:

slot-constraint has_host has-value Organism
slot-constraint has_host_part has-value OrganismPart

used in slots:

has_host
has_host_part

class Humidity

documentation:

The humidity that the biosource is exposed to.

type:

primitive

superclasses:

CultureCondition

class Individual

documentation:

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

type:

primitive

superclasses:

BiosourceProperty

class IndividualGeneticCharacterstics

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

class Infection

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

slot-constraint infected_by has-value Organism

class LabeledExtract

documentation:

The biosample after labeling for detection of the nucleic acids.

type:

primitive

superclasses:

BiomaterialState

constraints:

slot-constraint has_been_manipulated_by has-value BiomaterialPreparation

class Light

documentation:

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

type:

primitive

superclasses:

CultureCondition

class MassUnit

documentation:

Units used for mass measurements.

type:

primitive

superclasses:

Unit

used in individuals:

fg
g
kg
mg
ng
pg
ug

class Measurement

documentation:

Measured values and units.

type:

primitive

constraints:

slot-constraint has_units has-value Unit
slot-constraint value has-value top
slot-constraint measurement_type has-value one-of (change absolute)

used in classes:

Age
BiomaterialPreparation
ClinicalHistory
CompoundBasedTreatment
CultureCondition

used in slots:

measurement_type

class Medium

documentation:

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

type:

primitive

superclasses:

CultureCondition

class Modification

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

slot-constraint modification_type has-value one-of (addition rearrangement removal)

known subclasses:

GeneticModification
SomaticModification

used in classes:

GeneticModification
SomaticModification

class Nutrients

documentation:

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

type:

primitive

superclasses:

CultureCondition

constraints:

slot-constraint nutrient_component has-value Compound

used in classes:

Starvation

class OntologyEntry

documentation:

Controlled vocabulary or ontology that can be referred to.

type:

primitive

superclasses:

Resource

constraints:

slot-constraint value has-value top
slot-constraint description has-value top
slot-constraint ID has-value top
slot-constraint has_database_entry has-value DatabaseEntry

known subclasses:

BiosourceOntologyEntry
Compound

used in classes:

BiosourceOntologyEntry
Compound

class Organism

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

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

documentation:

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

type:

primitive

superclasses:

Contact

constraints:

slot-constraint name has-value top

used in classes:

BiosourceProvider
Person

class PastMedicalHistory

documentation:

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

type:

primitive

superclasses:

ClinicalHistory

class PathogenTests

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint tested_for has-value Organism
slot-constraint result_summary has-value one-of (inconclusive positive negative)

class Person

documentation:

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

type:

primitive

superclasses:

Contact

constraints:

slot-constraint first_name has-value top
slot-constraint has_affiliation has-value Organization
slot-constraint last_name has-value top
slot-constraint mid_initials has-value top

used in classes:

BiosourceProvider

class Preservation

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint preservation_type has-value one-of (seed_dormancy frozen_storage)
slot-constraint has_protocol has-value Protocol

class Protocol

documentation:

Documentation of the set of steps taken in a procedure.

type:

primitive

constraints:

slot-constraint has_hardware has-value Hardware
slot-constraint description has-value top
slot-constraint name has-value top
slot-constraint has_citation has-value BibliographicReference
slot-constraint has_software has-value Software

used in classes:

BiomaterialPreparation
CompoundBasedTreatment
ContaminantOrganism
Preservation
Treatment
Water

class QuantityUnit

documentation:

Units used for quantity measurements.

type:

primitive

superclasses:

Unit

used in individuals:

amol
fmol
mol
molecules
nmol
pmol
umol

class Resource

documentation:

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

type:

primitive

known subclasses:

BibliographicReference
Contact
DatabaseEntry
OntologyEntry

used in classes:

BibliographicReference
Contact
DatabaseEntry
OntologyEntry

class Sex

documentation:

The gender of the organism or the reproductive organs present on the organism (prior to any modification) that the biomaterial is derived from.

type:

primitive

superclasses:

BiosourceProperty

used in individuals:

both_sexes
female
male
unknown_sex

class Software

documentation:

The software application used.

type:

primitive

used in classes:

Protocol

class SomaticModification

documentation:

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

type:

primitive

superclasses:

Modification

constraints:

slot-constraint has_part_modified has-value OrganismPart

class Starvation

documentation:

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

type:

primitive

superclasses:

Treatment

constraints:

slot-constraint starved_of has-value Nutrients

class StrainOrLine

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

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

documentation:

The temperature that a biosource is exposed to.

type:

primitive

superclasses:

CultureCondition

class TemperatureUnit

documentation:

Units used for temperature measurements.

type:

primitive

superclasses:

Unit

used in individuals:

degrees_C
degrees_F
degrees_K

class TimeUnit

documentation:

Units used for time measurements.

type:

primitive

superclasses:

Unit

used in individuals:

days
hours
minutes
months
ms
seconds
us
weeks
years

class Treatment

documentation:

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

type:

primitive

superclasses:

BiomaterialManipulation

constraints:

slot-constraint has_protocol has-value Protocol

known subclasses:

BehavioralStimulus
CompoundBasedTreatment
Infection
Modification
Starvation

used in classes:

BehavioralStimulus
Biosample
CompoundBasedTreatment
Infection
Modification
Starvation

class URI

documentation:

Uniform Resource Identifier

type:

primitive

used in classes:

BibliographicReference
Contact
DatabaseEntry

used in individuals:

chem.sis.nlm.nih.gov/chemidplus
flybase.bio.indiana.edu/.bin/cvreport.html?id=
www.cabri.org/CABRI/home/guidelines/catalogue/CPCel%20linenamesahc.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.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=

class Unit

documentation:

Units of measure.

type:

primitive

known subclasses:

ConcentrationUnit
DistanceUnit
MassUnit
QuantityUnit
TemperatureUnit
TimeUnit
VolumeUnit

used in classes:

ConcentrationUnit
DistanceUnit
MassUnit
Measurement
QuantityUnit
TemperatureUnit
TimeUnit
VolumeUnit

class VolumeUnit

documentation:

Units used for volume measurements.

type:

primitive

superclasses:

Unit

used in individuals:

cc
dl
fl
l
ml
nl
pl
ul

class Water

documentation:

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

type:

primitive

superclasses:

EnvironmentalHistory

constraints:

slot-constraint has_additive has-value Compound
slot-constraint has_treatment has-value Protocol

slot ID

documentation:

used in classes:

BiosourceOntologyEntry
OntologyEntry

slot accession

documentation:

properties:

functional

used in classes:

DatabaseEntry

slot accession_version

documentation:

properties:

functional

used in classes:

DatabaseEntry

slot address

documentation:

used in classes:

Contact

slot authors

documentation:

used in classes:

BibliographicReference

slot biomaterial_amount

documentation:

used in classes:

BiomaterialPreparation

slot biomaterial_purity

documentation:

used in classes:

BiomaterialPreparation

slot biosource_type

documentation:

domain:

BiosourceProvider

properties:

functional

used in classes:

BiosourceProvider

slot description

documentation:

used in classes:

BarrierFacility
BiosourceOntologyEntry
OntologyEntry
Protocol

slot editor

documentation:

used in classes:

BibliographicReference

slot email

documentation:

used in classes:

Contact

slot fax

documentation:

used in classes:

Contact

slot first_name

documentation:

used in classes:

Person

slot gene_modified

documentation:

used in classes:

GeneticModification

slot has_URI

documentation:

properties:

functional

used in classes:

BibliographicReference
Contact
DatabaseEntry

slot has_additive

documentation:

used in classes:

Water

slot has_affiliation

documentation:

used in classes:

Person

slot has_been_manipulated_by

documentation:

properties:

functional

used in classes:

BiomaterialState
Biosample
Biosource
LabeledExtract

slot has_category

documentation:

slot has_citation

documentation:

used in classes:

Protocol

slot has_clinical_information

documentation:

used in classes:

ClinicalHistory

slot has_compound

documentation:

used in classes:

CompoundBasedTreatment

slot has_compound_measurement

documentation:

used in classes:

CompoundBasedTreatment

slot has_database_entry

documentation:

used in classes:

BiosourceOntologyEntry
Gene
OntologyEntry

slot has_donor

documentation:

properties:

functional

used in classes:

BiosourceProvider

slot has_hardware

documentation:

used in classes:

Protocol

slot has_host

documentation:

domain:

Host

used in classes:

Host

slot has_host_part

documentation:

domain:

Host

used in classes:

Host

slot has_lab_values

documentation:

used in classes:

ClinicalHistory

slot has_manufacturer

documentation:

used in classes:

Hardware

slot has_measurement

documentation:

used in classes:

Age
CultureCondition

slot has_owner

documentation:

properties:

functional

used in classes:

BiosourceProvider

slot has_part_modified

documentation:

used in classes:

SomaticModification

slot has_protocol

documentation:

used in classes:

BiomaterialPreparation
CompoundBasedTreatment
Preservation
Treatment

slot has_software

documentation:

used in classes:

Protocol

slot has_time_of_day

documentation:

used in classes:

BiomaterialPreparation

slot has_treatment

documentation:

used in classes:

Water

slot has_units

documentation:

used in classes:

Measurement

slot infected_by

documentation:

used in classes:

Infection

slot initial_time_point

documentation:

domain:

Age

properties:

functional

used in classes:

Age

slot is_contaminated_by

documentation:

used in classes:

ContaminantOrganism

slot is_decontaminated_by

documentation:

domain:

ContaminantOrganism

used in classes:

ContaminantOrganism

slot is_solvent

documentation:

used in classes:

Compound

slot issue

documentation:

domain:

BibliographicReference

used in classes:

BibliographicReference

slot last_name

documentation:

used in classes:

Person

slot make

documentation:

domain:

Hardware

used in classes:

Hardware

slot measurement_type

documentation:

domain:

Measurement

used in classes:

Measurement

slot mid_initials

documentation:

used in classes:

Person

slot model

documentation:

domain:

Hardware

used in classes:

Hardware

slot modification_type

documentation:

used in classes:

Modification

slot name

documentation:

used in classes:

Organization
Protocol

slot nutrient_component

documentation:

used in classes:

Nutrients

slot pages

documentation:

domain:

BibliographicReference

used in classes:

BibliographicReference

slot part_modified

documentation:

slot pathological_staging

documentation:

used in classes:

BiomaterialPreparation

slot phone

documentation:

used in classes:

Contact

slot preservation_type

documentation:

used in classes:

Preservation

slot publication

documentation:

used in classes:

BibliographicReference

slot publisher

documentation:

used in classes:

BibliographicReference

slot rating

documentation:

used in classes:

BarrierFacility

slot result_summary

documentation:

used in classes:

PathogenTests

slot starved_of

documentation:

used in classes:

Starvation

slot tested_for

documentation:

used in classes:

PathogenTests

slot title

documentation:

used in classes:

BibliographicReference

slot toll_free_phone

documentation:

used in classes:

Contact

slot treatment_application

documentation:

used in classes:

CompoundBasedTreatment

slot value

documentation:

properties:

functional

used in classes:

BiosourceOntologyEntry
Measurement
OntologyEntry

slot version

documentation:

slot volume

documentation:

domain:

BibliographicReference

used in classes:

BibliographicReference

slot year

documentation:

used in classes:

BibliographicReference

individual A

instance of:

DistanceUnit

individual CABRI

instance of:

CellLine

relations:

has_database_entry CABRI_linenamesahc

individual CABRI_linenamesahc

instance of:

DatabaseEntry

relations:

has_URI www.cabri.org/CABRI/home/guidelines/catalogue/CPCel%20linenamesahc.html

used in individuals:

CABRI

individual CASRegistryNumber

instance of:

Compound

relations:

has_database_entry ChemID

individual CBIL_CV

instance of:

TargetedCellType
OrganismPart

relations:

has_database_entry CBIL_anat_id

individual CBIL_anat_id

instance of:

DatabaseEntry

relations:

has_URI www.cbil.upenn.edu/servlet/allgenes-dev/servlet?page=anat&id=

used in individuals:

CBIL_CV

individual ChemID

instance of:

DatabaseEntry

relations:

has_URI chem.sis.nlm.nih.gov/chemidplus

used in individuals:

CASRegistryNumber

individual FlyBase

instance of:

TargetedCellType
OrganismPart

relations:

has_database_entry FlyBase_cv_id

individual FlyBase_cv_id

instance of:

DatabaseEntry

relations:

has_URI flybase.bio.indiana.edu/.bin/cvreport.html?id=

used in individuals:

FlyBase

individual IUPAC

instance of:

Compound

individual IntlComStdGenNomMice_Strains

instance of:

StrainOrLine

relations:

has_database_entry JAX_mouse_strains

individual JAX_mouse_strains

instance of:

DatabaseEntry

relations:

has_URI www.informatics.jax.org/external/festing/mouse/STRAINS.shtml

used in individuals:

IntlComStdGenNomMice_Strains

individual M

instance of:

ConcentrationUnit

individual MAD_stage

instance of:

DatabaseEntry

relations:

has_URI www.informatics.jax.org/mgihome/GXD/AD/

used in individuals:

MouseAnatomicalDictionary

individual MouseAnatomicalDictionary

instance of:

DevelopmentalStage
TargetedCellType
OrganismPart

relations:

has_database_entry MAD_stage

individual NCBI_taxon_id

instance of:

DatabaseEntry

relations:

has_URI www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=

used in individuals:

NCBI_taxonomy

individual NCBI_taxonomy

instance of:

Organism

relations:

has_database_entry NCBI_taxon_id

individual absolute

used in classes:

Measurement

individual addition

used in classes:

Modification

individual amol

instance of:

QuantityUnit

individual beginning_of_stage

used in classes:

Age

individual biopsy

used in classes:

BiosourceProvider

individual both_sexes

instance of:

Sex

individual cc

instance of:

VolumeUnit

individual change

used in classes:

Measurement

individual chem.sis.nlm.nih.gov/chemidplus

instance of:

URI

used in individuals:

ChemID

individual cm

instance of:

DistanceUnit

individual days

instance of:

TimeUnit

individual degrees_C

instance of:

TemperatureUnit

individual degrees_F

instance of:

TemperatureUnit

individual degrees_K

instance of:

TemperatureUnit

individual dl

instance of:

VolumeUnit

individual fM

instance of:

ConcentrationUnit

individual female

instance of:

Sex

individual fg

instance of:

MassUnit

individual fl

instance of:

VolumeUnit

individual flybase.bio.indiana.edu/.bin/cvreport.html?id=

instance of:

URI

used in individuals:

FlyBase_cv_id

individual fmol

instance of:

QuantityUnit

individual frozen_storage

used in classes:

Preservation

individual g

instance of:

MassUnit

individual g/l

instance of:

ConcentrationUnit

individual hours

instance of:

TimeUnit

individual in_situ

used in classes:

CompoundBasedTreatment

individual in_vitro

used in classes:

CompoundBasedTreatment

individual in_vivo

used in classes:

CompoundBasedTreatment

individual inconclusive

used in classes:

PathogenTests

individual kg

instance of:

MassUnit

individual l

instance of:

VolumeUnit

individual m

instance of:

DistanceUnit

individual mM

instance of:

ConcentrationUnit

individual male

instance of:

Sex

individual mg

instance of:

MassUnit

individual mg/ml

instance of:

ConcentrationUnit

individual minutes

instance of:

TimeUnit

individual ml

instance of:

VolumeUnit

individual ml/l

instance of:

ConcentrationUnit

individual mm

instance of:

DistanceUnit

individual mol

instance of:

QuantityUnit

individual molecules

instance of:

QuantityUnit

individual months

instance of:

TimeUnit

individual ms

instance of:

TimeUnit

individual negative

used in classes:

PathogenTests

individual ng

instance of:

MassUnit

individual nl

instance of:

VolumeUnit

individual nm

instance of:

DistanceUnit

individual nmol

instance of:

QuantityUnit

individual no

used in classes:

Compound

individual pM

instance of:

ConcentrationUnit

individual paraffin_section

used in classes:

BiosourceProvider

individual percent_vol/vol

instance of:

ConcentrationUnit

individual percent_weight/vol

instance of:

ConcentrationUnit

individual percent_weight/weight

instance of:

ConcentrationUnit

individual pg

instance of:

MassUnit

individual pl

instance of:

VolumeUnit

individual planting

used in classes:

Age

individual pmol

instance of:

QuantityUnit

individual positive

used in classes:

PathogenTests

individual postmortem

used in classes:

BiomaterialPreparation

individual premortem

used in classes:

BiomaterialPreparation

individual rearrangement

used in classes:

Modification

individual removal

used in classes:

Modification

individual seconds

instance of:

TimeUnit

individual seed_dormancy

used in classes:

Preservation

individual uM

instance of:

ConcentrationUnit

individual ug

instance of:

MassUnit

individual ul

instance of:

VolumeUnit

individual um

instance of:

DistanceUnit

individual umol

instance of:

QuantityUnit

individual unknown_sex

instance of:

Sex

individual us

instance of:

TimeUnit

individual weeks

instance of:

TimeUnit

individual www.cabri.org/CABRI/home/guidelines/catalogue/CPCel%20linenamesahc.html

instance of:

URI

used in individuals:

CABRI_linenamesahc

individual www.cbil.upenn.edu/servlet/allgenes-dev/servlet?page=anat&id=

instance of:

URI

used in individuals:

CBIL_anat_id

individual www.informatics.jax.org/external/festing/mouse/STRAINS.shtml

instance of:

URI

used in individuals:

JAX_mouse_strains

individual www.informatics.jax.org/mgihome/GXD/AD/

instance of:

URI

used in individuals:

MAD_stage

individual www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=

instance of:

URI

used in individuals:

NCBI_taxon_id

individual years

instance of:

TimeUnit

individual yes

used in classes:

Compound

Axioms

Documentation generated: Sun Dec 02 17:57:39 EST 2001