Ontology Container Information

Title:
"An MGED Ontology for Biomaterial"
Creator:
Chris Stoeckert and Helen Parkinson
Description:
Description of the sample (biomaterial) used in a microarray experiment.
Release:
"1.3"
Classes:
83
Slots:
75
Individuals:
121
Axioms:
0

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 CultureCondition CurrentDiseaseHistory DatabaseEntry DensityRange DevelopmentalStage DiseaseState DistanceUnit EnvironmentalHistory FamilyHistory Gender Gene Generations GeneticModification GeneticVariation Genotype Haplotype Hardware Host Humidity Individual IndividualGeneticCharacterstics Infection LabeledExtract Light MassUnit Measurement Medium Modification Nutrients OntologyEntry Organism OrganismPart Organization PastMedicalHistory PathogenTests Person Polymorphism Preservation Protocol QuantityUnit Resource Sex Software SomaticModification Starvation StrainOrLine TargetedCellType Temperature TemperatureUnit TimeUnit Treatment URI Unit User VolumeUnit Water

Slots

ID accession accession_version address authors biomaterial_amount biomaterial_purity biosource_type description editor email fax first_name gene_modified has_URI has_additive has_affiliation has_been_manipulated_by has_category has_citation has_clinical_information has_compound has_compound_measurement has_database_entry has_delivery_method has_donor has_hardware has_host has_host_part has_lab_value has_manufacturer has_measurement has_owner has_part_modified has_protocol has_software has_time_of_day has_treatment has_units has_vehicle infected_by initial_time_point is_contaminated_by is_decontaminated_by is_solvent is_user_defined issue last_name make matrix_used measurement_type mid_initials model modification_type name nutrient_component pages part_modified pathological_staging phone preservation_type publication publisher rating result_summary starved_of tested_for title toll_free_phone treatment_application value version volume was_prepared_by year

Individuals

A CABRI CABRI_linenamesahc CASRegistryNumber CBIL_CV CBIL_anat_id ChemID F+ F- FlyBase FlyBase_cv_id Hfr IUPAC IntlComStdGenNomMice_Strains JAX_mouse_strains M MAD_stage MouseAnatomicalDictionary NCBI_taxon_id NCBI_taxonomy SPF absolute ad libitum addition agar amol beginning_of_stage biopsy birth blood_sample cc change chem.sis.nlm.nih.gov/chemidplus cm coitus days degrees_C degrees_F degrees_K dl fM feeding female fg fl flybase.bio.indiana.edu/.bin/cvreport.html?id= fmol frozen_section frozen_storage g g/l hermaphrodite hours in_situ in_vitro in_vivo inconclusive intramuscular intraperitoneal intravenous kg l liquid m mM male mating_type_a mating_type_alpha mg mg/ml minutes mixed_sex ml ml/l mm mol molecules months ms negative ng nl nm nmol no non-SPF oral_gavage pM paraffin_section percent_vol/vol percent_weight/vol percent_weight/weight pg pl planting pmol positive postmortem premortem rearrangement removal seconds seed_dormancy semisolid soil subcutaneous uM ug ul um umol unknown_sex us weeks 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= years yes

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 initial_time_point has-value one-of (beginning_of_stage coitus birth planting)
slot-constraint has_measurement has-value Measurement
used in slots:
initial_time_point

class Allele

type:
primitive
superclasses:
IndividualGeneticCharacterstics

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

documentation:
Measurements that relate only to any biomaterial quantifiable, not for compound or general measurement
type:
primitive
superclasses:
Measurement

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 was_prepared_by has-value User
slot-constraint pathological_staging has-value one-of (postmortem premortem)
slot-constraint has_protocol has-value Protocol
slot-constraint biomaterial_amount has-value Measurement
slot-constraint biomaterial_purity has-value range 100 0)
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:
BiosourceProperty
OntologyEntry
constraints:
slot-constraint ID has-value top
slot-constraint description has-value top
slot-constraint value has-value top
slot-constraint has_database_entry has-value 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

documentation:
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
type:
primitive
superclasses:
BiomaterialDescription
constraints:
slot-constraint is_user_defined has-value User
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_donor has-value Organization
slot-constraint has_owner has-value Person
slot-constraint biosource_type has-value one-of (frozen_section paraffin_section blood_sample 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 CellType

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

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 as bacground information relevant to the experiment.
type:
primitive
superclasses:
EnvironmentalHistory
constraints:
slot-constraint has_clinical_information has-value ClinicalInformation
slot-constraint has_lab_value has-value Measurement
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 (yes no)
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:
one-of (intraperitoneal)
Treatment
constraints:
slot-constraint has_delivery_method has-value one-of (oral_gavage feeding ad libitum subcutaneous intravenous intramuscular)
slot-constraint has_vehicle has-value Compound
slot-constraint treatment_application has-value one-of (in_vitro in_situ in_vivo)
slot-constraint has_protocol has-value Protocol
slot-constraint has_compound_measurement has-value Measurement
slot-constraint has_compound has-value Compound

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 fax has-value top
slot-constraint email has-value top
slot-constraint address has-value top
slot-constraint has_URI has-value URI
slot-constraint phone has-value top
slot-constraint toll_free_phone has-value top
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 accession_version has-value top
slot-constraint has_URI has-value URI
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
Nutrients
PathogenTests
Preservation
Water
used in classes:
BarrierFacility
Bedding
Biosource
ClinicalHistory
CultureCondition
FamilyHistory
Nutrients
PathogenTests
Preservation
Water

class FamilyHistory

documentation:
Relevant aspects of genetic preconditions or family members clinical history.
type:
primitive
superclasses:
EnvironmentalHistory

class Gender

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

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 Genotype

type:
primitive
superclasses:
IndividualGeneticCharacterstics

class Haplotype

type:
primitive
superclasses:
IndividualGeneticCharacterstics

class Hardware

documentation:
The machine or instrument used.
type:
primitive
constraints:
slot-constraint make has-value top
slot-constraint has_manufacturer has-value Contact
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
constraints:
slot-constraint ID has-value top

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
known subclasses:
Allele
Genotype
Haplotype
Polymorphism
used in classes:
Allele
Genotype
Haplotype
Polymorphism

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 value has-value top
slot-constraint has_units has-value Unit
slot-constraint measurement_type has-value one-of (change absolute)
known subclasses:
BiomaterialMeasurement
used in classes:
Age
BiomaterialMeasurement
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
constraints:
slot-constraint matrix_used has-value one-of (semisolid liquid agar soil)

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 (rearrangement removal addition)
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
EnvironmentalHistory
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 ID has-value top
slot-constraint description has-value top
slot-constraint value 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:
one-of (non-SPF SPF)
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 has_affiliation has-value Organization
slot-constraint first_name has-value top
slot-constraint mid_initials has-value top
slot-constraint last_name has-value top
known subclasses:
User
used in classes:
BiosourceProvider
User

class Polymorphism

type:
primitive
superclasses:
IndividualGeneticCharacterstics

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_citation has-value BibliographicReference
slot-constraint name has-value top
slot-constraint description has-value top
slot-constraint has_hardware has-value Hardware
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:
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

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 User

documentation:
User defined term not present in external ontology or MGED list of biosource properties, like age sex etc
type:
primitive
superclasses:
Person
constraints:
slot-constraint ID has-value top
used in classes:
BiomaterialPreparation
BiosourceProperty

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

slot ID

documentation:
used in classes:
BiosourceOntologyEntry
Individual
OntologyEntry
User

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_delivery_method

documentation:
used in classes:
CompoundBasedTreatment

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_value

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 has_vehicle

documentation:
used in classes:
CompoundBasedTreatment

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 is_user_defined

documentation:
used in classes:
BiosourceProperty

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 matrix_used

documentation:
used in classes:
Medium

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 was_prepared_by

documentation:
used in classes:
BiomaterialPreparation

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:
OrganismPart
TargetedCellType
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 F+

instance of:
Sex

individual F-

instance of:
Sex

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 Hfr

instance of:
Sex

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:
TargetedCellType
DevelopmentalStage
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 SPF

used in classes:
PathogenTests

individual absolute

used in classes:
Measurement

individual ad libitum

used in classes:
CompoundBasedTreatment

individual addition

used in classes:
Modification

individual agar

used in classes:
Medium

individual amol

instance of:
QuantityUnit

individual beginning_of_stage

used in classes:
Age

individual biopsy

used in classes:
BiosourceProvider

individual birth

used in classes:
Age

individual blood_sample

used in classes:
BiosourceProvider

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 coitus

used in classes:
Age

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 feeding

used in classes:
CompoundBasedTreatment

individual female

instance of:
Gender

individual fg

instance of:
MassUnit

individual fl

instance of:
VolumeUnit