contributor
has column label: contributor

description
has column label: description

license
has column label: license

title
has column label: title

contactPoint
has column label: contact_point

endedAtTime
has column label: end_time

generated
has column label: generated

hadDerivation
type: ObjectProperty
inverse of: wasDerivedFrom
definition: Inverse of prov:wasDerivedFrom
has column label: derivation

used
inverse of: wasUsedBy
has column label: used

wasAssociatedWith
has column label: associated_with

wasDerivedFrom
has column label: derived_from

wasGeneratedBy
has column label: generated_by

TerraCore
type: Ontology
creator: Kathy Reinold
date: 20 Jul 2020
license: LICENSE
comment: Please cite The Broad Institute of Harvard and MIT, Data Sciences Platform.
imports: EFO subset
imports: NCBITaxon Organisms subset
imports: OBIAssay subset
imports: OBI core
imports: TerraCoreValueSets
imports: TerraDCAT ap
version info: Version 1.0.0

Activity
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: created
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: endedAtTime
subclass of: Restriction
  max cardinality: 1
  on property: startedAtTime
subclass of: Restriction
  min cardinality: 0
  on property: wasAssociatedWith
subclass of: Restriction
  min cardinality: 0
  on property: hasProtocol
subclass of: Restriction
  min cardinality: 0
  on property: usesSample
subclass of: Restriction
  min cardinality: 1
  on property: generated
subclass of: Restriction
  min cardinality: 1
  on property: used
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: An activity occurs over a period of time, generates an entity, and may include consuming, processing, transforming, modifying, relocating, or using entities. This subclass of prov:Activity restricts members to those with a DataModality relevant to biomedical research.

Address
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  cardinality: 1
  on property: hasPostalCode
subclass of: Restriction
  max cardinality: 1
  on property: hasCountry
definition: A physical address for a Person or Organization.

Age
type: Class
subclass of: OBI_0001167
subclass of: Restriction
  cardinality: 1
  on property: hasAgeCategory
subclass of: Restriction
  max cardinality: 1
  on property: hasLowerBound
subclass of: Restriction
  max cardinality: 1
  on property: hasUpperBound
equivalent class: Restriction
  max cardinality: 1
  on property: hasAgeUnit

Alignment
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: endedAtTime
subclass of: Restriction
  min cardinality: 0
  on property: usesSample
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  min cardinality: 1
  on property: usesReferenceAssembly
subclass of: Restriction
  on property: generated
  some values from: AlignmentFile
subclass of: Restriction
  on property: used
  some values from: SoftwareAgent
subclass of: Restriction
  on property: used
  some values from: SequenceFile
disjoint with: Analysis
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Sequencing
disjoint with: VariantCallingActivity
definition: An activity that aligns the output of a Sequencing Activity (a genetic sequence) to produce an aligned sequence.

AlignmentFile
type: Class
subclass of: File
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  cardinality: 1
  on property: usesReferenceAssembly
subclass of: Restriction
  max cardinality: 1
  on property: hasPercentAlignedReads
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: An electronic record of the alignment of a genetic sequence for a particular Sample compared with a reference sequence generated by an AlignmentActivity.

Analysis
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  on property: generated
  some values from: File
subclass of: Restriction
  on property: used
  some values from: SoftwareAgent
subclass of: Restriction
  on property: used
  some values from: File
disjoint with: Alignment
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Sequencing
disjoint with: VariantCallingActivity
definition: An activity that records the output of a specific analysis method. Software version, components, arguments are described in prov:SoftwareAgent.

Antibody
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  cardinality: 1
  on property: has host organism
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasTarget
definition: A reference to the antibody/antibodies used in this Activity.

Assay
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: usesSample
subclass of: Restriction
  min cardinality: 1
  on property: hasAssayType
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  on property: generated
  some values from: File
disjoint with: Alignment
disjoint with: Analysis
disjoint with: LibraryPreparation
disjoint with: Sequencing
disjoint with: VariantCallingActivity
definition: An activity that generates an electronic record documenting the result of the Assay performed.

BioSample
type: Class
subclass of: Sample
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: source
subclass of: Restriction
  max cardinality: 1
  on property: hasAnatomicalSite
subclass of: Restriction
  max cardinality: 1
  on property: hasDonorAgeAtCollection
subclass of: Restriction
  max cardinality: 1
  on property: hasPreservationState
subclass of: Restriction
  min cardinality: 0
  on property: wasDerivedFrom
subclass of: Restriction
  min cardinality: 0
  on property: hasCrossReference
subclass of: Restriction
  min cardinality: 0
  on property: has genetic modification
subclass of: Restriction
  min cardinality: 0
  on property: has genetic modification method
subclass of: Restriction
  min cardinality: 0
  on property: has genetic modification type
subclass of: Restriction
  min cardinality: 1
  on property: wasUsedBy
subclass of: Restriction
  min cardinality: 1
  on property: hasDonor
subclass of: Restriction
  on property: wasUsedBy
  some values from: Activity
equivalent class: Restriction
  cardinality: 1
  on property: hasBioSampleType
alternative label: Biospecimen
alternative label: Sample
alternative label: Specimen from organism
definition: Data about a physical sample consisting of one or more cells taken from an organism (living or deceased) or derived from such a Sample.

BioSampleDissociation
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
equivalent class: EFO_0009091
definition: Activity which results in the separation of a BioSample into individual cells or a cell suspension.

Biological sex
type: Class
subclass of: BFO_0000019
subclass of: PATO_0001894
definition: A quality of an organism indicating physical sexual characteristics. Equivalent of PATO's phenotypic sex but pseudohermaphrodite is not relevant to existing data and is not recommended.

Country
type: Class
subclass of: SpatialThing
definition: A country represented by the ISO-3166 Alpha-2 code and name (as a label). https://www.iso.org/obp/ui/#search

Diagnosis
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: age at diagnosis
subclass of: Restriction
  max cardinality: 1
  on property: age at onset
definition: Result of a medical investigation that often identies a disease or condition.

Dog
type: NCBITaxon 9615

DogDonor
type: Class
subclass of: Donor
subclass of: Restriction
  cardinality: 1
  on property: id
equivalent class: Restriction
  has value: Dog
  on property: hasOrganismType
definition: Extension of Donor class for dogs.

Donor
type: Class
subclass of: OBI_0100026
subclass of: Restriction
  cardinality: 1
  on property: hasOrganismType
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: hasAgeAtDeath
subclass of: Restriction
  max cardinality: 1
  on property: age at diagnosis
subclass of: Restriction
  max cardinality: 1
  on property: hasPhenotypicSex
subclass of: Restriction
  max cardinality: 1
  on property: hasSexAssignedAtBirth
subclass of: Restriction
  min cardinality: 0
  on property: has BioSample
subclass of: Restriction
  min cardinality: 0
  on property: hasCrossReference
subclass of: Restriction
  min cardinality: 0
  on property: hasFamilyIdentifier
subclass of: Restriction
  min cardinality: 0
  on property: hasParent
subclass of: Restriction
  min cardinality: 0
  on property: hasSibling
subclass of: Restriction
  on property: isPartOf
  some values from: Dataset
definition: An organism from which a sample or test result is available

Donor Treatment
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: hasTreatmentType
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: hasDonorAgeAtCollection
subclass of: Restriction
  min cardinality: 0
  on property: has dose
subclass of: Restriction
  min cardinality: 0
  on property: has duration
subclass of: Restriction
  min cardinality: 0
  on property: has duration unit
subclass of: Restriction
  min cardinality: 0
  on property: has medication
subclass of: Restriction
  min cardinality: 0
  on property: has treatment outcome
definition: Activities or processes undertaken with the expectation of therapeutic value to the Donor.

Dose
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  all values from: decimal
  on property: value
subclass of: Restriction
  cardinality: 1
  on property: value
subclass of: Restriction
  cardinality: 1
  on property: hasUnit
definition: A measured amount of a substance.

Experiment
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: An operation or procedure carried out under controlled conditions to make a discovery or to test or establish a hypothesis. In the context of this data model, an experiment is a collection of related activities, possibly including sample preparation, sequencing, assays and/or downstream analysis.

Family Member
type: Class
subclass of: OBI_0100026
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  has value: Human
  on property: hasOrganismType
subclass of: Restriction
  max cardinality: 1
  on property: hasAgeAtDeath
subclass of: Restriction
  max cardinality: 1
  on property: hasPhenotypicSex
subclass of: Restriction
  max cardinality: 1
  on property: hasSexAssignedAtBirth
subclass of: Restriction
  min cardinality: 0
  on property: has genetic ancestry
subclass of: Restriction
  min cardinality: 0
  on property: hasGenotypicSex
subclass of: Restriction
  min cardinality: 0
  on property: has manner of death
subclass of: Restriction
  min cardinality: 0
  on property: hasRace
definition: Family member has biological relationship to a Donor. Limited health information. A family member for whom samples, imaging studies, lab tests or other healthcare information is available may be considered a Donor.

Female

Female
type: Class
has exact synonym: F
subclass of: Biological sex
equivalent class: PATO_0000383
alternative label: F

File
type: Class
comment: Used definition from http://semanticscience.org/resource/SIO_000396 but equivalence to http://www.w3.org/ns/dcat#Distribution doesn't make sense in this context; thus we have our own class. Also added electronic.
subclass of: IAO_0000030
subclass of: Restriction
  cardinality: 1
  on property: byteSize
subclass of: Restriction
  cardinality: 1
  on property: hasFileFormat
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: has checksum
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  on property: hasCrossReference
  some values from: anyURI
definition: A file is an information-bearing electronic object that contains a physical embodiment of some information using a particular character encoding.

GRCh37
type: ReferenceAssembly
hasGRCName: GRCh37
hasOrganismType: Human

General Research Use
type: DUO_0000005

GRCh38
type: ReferenceAssembly
hasGRCName: GRCh38
hasOrganismType: Human

Histopathology
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: confirmsDisease
subclass of: Restriction
  max cardinality: 1
  on property: hasGrade
subclass of: Restriction
  max cardinality: 1
  on property: hasStage
subclass of: Restriction
  max cardinality: 1
  on property: hasTumorMorphology
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
equivalent class: OBI_0002564
equivalent class: Restriction
  all values from: Datatype
    one of: tumor
    one of: normal
    one of: abnormal
    one of: peritumoral
  on property: hasTumorMorphology

Human
type: NCBITaxon 9606
definition: Instance of Homo sapiens organism to define organism type.
preferred label: Homo sapiens

HumanDonor
type: Class
subclass of: Donor
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  has value: Human
  on property: hasOrganismType
subclass of: Restriction
  max cardinality: 1
  on property: hasAgeAtDeath
subclass of: Restriction
  max cardinality: 1
  on property: hasPhenotypicSex
subclass of: Restriction
  max cardinality: 1
  on property: hasSexAssignedAtBirth
subclass of: Restriction
  min cardinality: 0
  on property: has BioSample
subclass of: Restriction
  min cardinality: 0
  on property: hasCrossReference
subclass of: Restriction
  min cardinality: 0
  on property: hasFamilyIdentifier
subclass of: Restriction
  min cardinality: 0
  on property: has measurement
subclass of: Restriction
  min cardinality: 0
  on property: hasParent
subclass of: Restriction
  min cardinality: 0
  on property: hasSibling
subclass of: Restriction
  min cardinality: 0
  on property: hasTreatment
subclass of: Restriction
  on property: isPartOf
  some values from: Dataset
definition: Extension of Donor class for Humans.

Intersex
type: Class
has exact synonym: intersex
subclass of: Biological sex
equivalent class: PATO_0001340
alternative label: Hermaphrodite

Library
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  cardinality: 1
  on property: wasGeneratedBy
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: hasAssay
subclass of: Restriction
  min cardinality: 1
  on property: wasUsedBy
definition: A collection of nucleic acid molecules.

LibraryPreparation
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: hasLibraryPreparationType
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  on property: generated
  some values from: Library
disjoint with: Alignment
disjoint with: Analysis
disjoint with: Assay
disjoint with: Sequencing
disjoint with: VariantCallingActivity
definition: Activity which results in the creation of a library from fragments of genomic material in preparation for further analysis.

Male

Male
type: Class
has exact synonym: M
subclass of: Biological sex
equivalent class: PATO_0000384
alternative label: M

Measurement
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  all values from: decimal
  on property: value
subclass of: Restriction
  cardinality: 1
  on property: value
subclass of: Restriction
  cardinality: 1
  on property: has measurement type
subclass of: Restriction
  cardinality: 1
  on property: has measurement type
subclass of: Restriction
  cardinality: 1
  on property: hasUnit
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: generated
subclass of: Restriction
  on property: generated
  some values from: File
definition: The record of the size, quantity or outcome of a clinical or laboratory test.

MolecularSample
type: Class
subclass of: Sample
subclass of: Restriction
  cardinality: 1
  on property: id
definition: Data about a physical sample consisting of one or more molecular entities, either purified from a Sample or synthesized.

MouseDonor
type: Class
subclass of: Donor
subclass of: Restriction
  cardinality: 1
  on property: id
equivalent class: Restriction
  has value: Mus musculus
  on property: hasOrganismType
definition: Extension of Donor class for mice.

Mus musculus
type: NCBITaxon_10090
definition: Instance of Mus musculus organism to define organism type.

NoRestriction
type: DUO_0000004

NucleusIsolation
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
equivalent class: EFO_0007831
definition: Activity to separate the nucleus or nuclei from the cell.

Principal Investigator
type: Class
subclass of: Person
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: title
subclass of: Restriction
  min cardinality: 1
  on property: family name
subclass of: Restriction
  min cardinality: 1
  on property: givenname
subclass of: Restriction
  min cardinality: 1
  on property: mbox
definition: The principal or lead person who carries out an investigation assigned by a sponsor or authorizing agent.

Project
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: description
subclass of: Restriction
  cardinality: 1
  on property: title
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: contributor
subclass of: Restriction
  min cardinality: 0
  on property: isReferencedBy
subclass of: Restriction
  min cardinality: 0
  on property: hasCrossReference
subclass of: Restriction
  min cardinality: 0
  on property: isFundedBy
subclass of: Restriction
  min cardinality: 0
  on property: hasOriginalPublication
subclass of: Restriction
  min cardinality: 1
  on property: hasPrincipalInvestigator
definition: A collective effort with an objective related to biomedical research.

Rabbit
type: NCBITaxon 9986

ReferenceAssembly
type: Class
IAO_0000114: DRAFT
comment: Instances should include either a cross reference to the reference sequence or an official GRCName from the Genome Reference Consortium, or both.
subclass of: OBI_0001573
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: hasCrossReference
subclass of: Restriction
  min cardinality: 0
  on property: hasGRCName
subclass of: Restriction
  min cardinality: 1
  on property: hasOrganismType
definition: DNA sequence data identified as representative of specific organism's DNA.

Sample
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  cardinality: 1
  on property: hasDataUsePermission
subclass of: Restriction
  max cardinality: 1
  on property: has date collected
subclass of: Restriction
  min cardinality: 0
  on property: hadDerivation
subclass of: Restriction
  min cardinality: 0
  on property: hasDataUseModifier
subclass of: Restriction
  min cardinality: 1
  on property: isPartOf
subclass of: Restriction
  min qualified cardinality: 0
  on class: Sample
  on property: wasDerivedFrom
subclass of: Restriction
  min qualified cardinality: 1
  on class: Activity
  on property: wasUsedBy
subclass of: Restriction
  on property: isPartOf
  some values from: Dataset
definition: Data about a physical material collected for the purpose of research.

SampleTreatmentActivity
type: Class
subclass of: Activity
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: Activity which transforms a BioSample into another BioSample. Typically the sample treatment activity involves adding something to cells or tissue, for example, treatment with chemicals, drugs, biological infection, irradiation, exposures, or other non-genetic modifications. This treatment excludes mechanical separation of a BioSample into single cells (covered by BioSampleDissociation), and is not needed for genetic modifications to cells (covered by hasGeneticModification).

SequenceFile
type: Class
subclass of: File
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: hasLibraryLayout
subclass of: Restriction
  max cardinality: 1
  on property: hasPercentDuplicateFragments
subclass of: Restriction
  max cardinality: 1
  on property: hasReadCount
subclass of: Restriction
  max cardinality: 1
  on property: hasReadLength
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: An electronic record of the genetic sequence for a particular Sample generated by a SequencingActivity.

SequenceLocation
type: Class
subclass of: OBI_0000973
subclass of: Restriction
  cardinality: 1
  on property: hasStartPosition
subclass of: Restriction
  cardinality: 1
  on property: hasStopPosition
subclass of: Restriction
  min cardinality: 0
  on property: has chromosome
definition: The location of a sequence feature defined by its start and end position based on a reference coordinate system.

Sequencing
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: endedAtTime
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  min cardinality: 1
  on property: usesSample
subclass of: Restriction
  on property: generated
  some values from: SequenceFile
disjoint with: Alignment
disjoint with: Analysis
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: VariantCallingActivity
definition: An activity that produces an electronic record of a genetic sequence from a Sample

SingleCell
type: Class
subclass of: BioSample
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: hasAnatomicalRegion
definition: Data about a physical sample consisting of a single cell or nucleus taken from an organism (living or deceased) or derived from such a Sample.

SingleCellAssignment
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: An activity that infers a cell type based on analysis.

SingleCellIsolation
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
definition: Activity to separate individual cells or nuclei.

User Restriction
type: DUO_0000026

VariantCall
type: Class
subclass of: OBI_0000973
subclass of: Restriction
  cardinality: 1
  on property: hasAllele
subclass of: Restriction
  cardinality: 1
  on property: hasSequenceLocation
subclass of: Restriction
  min cardinality: 0
  on property: hasVariantReference
subclass of: Restriction
  min cardinality: 0
  on property: usesSample
subclass of: Restriction
  on property: used
  some values from: VariantCallSet
definition: A variation in genetic sequence for a particular Sample and VariantCallingActivity.

VariantCallSet
type: Class
subclass of: File
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: hasVariantCall
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  min cardinality: 1
  on property: usesReferenceAssembly
definition: An electronic record of a collection of variations in genetic sequence for a particular Sample that have been generated by a VariantCallingActivity.

VariantCallingActivity
type: Class
subclass of: Activity
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: usesSample
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  min cardinality: 1
  on property: usesReferenceAssembly
subclass of: Restriction
  on property: generated
  some values from: VariantCall
subclass of: Restriction
  on property: generated
  some values from: VariantCallSet
subclass of: Restriction
  on property: used
  some values from: SoftwareAgent
subclass of: Restriction
  on property: used
  some values from: AlignmentFile
disjoint with: Alignment
disjoint with: Analysis
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Sequencing
definition: An activity that identifies genetic sequence alterations in a Sample when compared to a reference.
preferred label: VariantCalling

Weight
type: Class
subclass of: IAO_0000109
equivalent class: PATO_0000128
definition: A measurement of the mass of an entity.

confirmsDisease
type: ObjectProperty
domain: Diagnosis
range:
  union of: OGMS_0000031
  union of: anyURI
definition: A property that identifies a disease or condition has been confirmed through diagnosis. Contrast with hasDisease.
has column label: confirms_disease

hasActivityType
type: DatatypeProperty
domain: Activity
range:
  union of: anyURI
  union of: string
definition: A reference to the type of activity, preferably using an identifier in a recommended standard ontology.
has column label: activity_type

hasAge
type: ObjectProperty
domain: BioSample
domain: Donor
domain: Family Member
range: Age
definition: A reference to the Age of the Donor at the point in time that data was collected or that the BioSample was obtained.
has column label: age

hasAgeAtDeath
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range: Age
definition: A reference to the Age of the Donor at time of death.
has column label: death_age

age at diagnosis
type: ObjectProperty
domain: Diagnosis
range: Age
definition: A reference to the Age of the Donor at the point in time that diagnosis was made.
has column label: diagnosis_age

age at onset
type: ObjectProperty
domain: Diagnosis
range: Age
definition: A reference to the Age of the Donor at the onset of the disease associated with the diagnosis.
has column label: onset_age

hasAgeCategory
type: DatatypeProperty
domain: Age
range: Datatype
  one of: Embryonic
  one of: Postnatal
has column label: age_category

hasAgeUnit
type: DatatypeProperty
domain: Age
range: Datatype
  one of: days
  one of: years
sub property of: hasUnit
definition: A reference to the unit of time during which an entity has existed.
has column label: age_unit

hasAlignedFragments
type: DatatypeProperty
comment: For alignment file types.
domain: AlignmentFile
range: integer

hasAllele
type: DatatypeProperty
domain: VariantCall
range: string

hasAlpha2Code
type: AnnotationProperty
domain: Country
range: string

has amount
type: DatatypeProperty
comment: Consider replacing with a measurement ontology
range: decimal
definition: A property that identifies the numerical quantity of an entity.
has column label: amount

has amount unit
type: DatatypeProperty
range: string
sub property of: hasUnit
definition: A property that captures the units of an entity. The units may be an amount such as moles or grams; or a concentration, such as g/mL or molarity. Other units may include enzyme activity, the specific activity of a radionucleotide, or the titer of an antibody
has column label: amount_unit

hasAnatomicalRegion
type: DatatypeProperty
comment: Many groups are convening to define Common Coordinate Frameworks for specific organs/species. This will be a rapidly evolving area in the near future. Thus allowing text or URI as we wait for the field to mature allows us to support what we hope will at a minimum be controlled vocabulary under discussion of these groups.
domain: BioSample
domain: SingleCell
range:
  union of: anyURI
  union of: string
definition: A reference to the physical location within the AnatomicalSite from which the BioSample was taken.
has column label: anatomical_region

hasAnatomicalSite
type: DatatypeProperty
comment: May want to consider restricting this to UBERON terms but currently any URI is allowed. This is useful for imaging and other whole body samples as UBERON does not have "whole body". Use NCIT:C13041 for this.
domain: BioSample
range:
  union of: anyURI
  union of: string
definition: A reference to the site within the organism from which the BioSample was taken.
has column label: anatomical_site

hasAprioriCellType
type: ObjectProperty
comment: Need definition
domain: SingleCell
range: CL_0000003

hasAssay
type: ObjectProperty
domain: BioSample
range: Assay
sub property of: wasUsedBy
definition: A subproperty of usedBy which indicates that an AssayActivity was performed using this entity.

hasAssayType
type: DatatypeProperty
domain:
  union of: Assay
  union of: Experiment
range:
  union of: OBI_0000070
  union of: string
  union of: anyURI
definition: A reference to the type of assay, preferably using an identifier in the Ontology for Biomedical Investigations assay entity (http://purl.obolibrary.org/obo/OBI_0000070).
has column label: assay_type

hasAverageReadLength
type: DatatypeProperty
comment: Need definition
domain: SequenceFile
range: decimal

has BioSample
type: ObjectProperty
domain: Donor
range: BioSample
inverse of: hasDonor
definition: This property references the BioSample donated by the Donor.
has column label: biosample

hasBioSampleType
type: ObjectProperty
comment: Need definition
domain: BioSample
range: BioSampleType
sub property of: hasSampleType
has column label: biosample_type

has birth year
type: Property
type: DatatypeProperty
comment: Need definition
domain: Donor
domain: Family Member
range: integer

hasCellCycle
type: DatatypeProperty
domain: SingleCell
range:
  union of: anyURI
  union of: string
definition: A property that describes the stage of the cell cycle at the time the sample was obtained.
has column label: cell_cycle

hasCellState
type: DatatypeProperty
domain: SingleCell
range:
  union of: anyURI
  union of: string
definition: A property that describes the cell’s metabolic or electrophysiological state.
has column label: cell_state

has checksum
type: DatatypeProperty
comment: Need definition
domain: File
range: string
preferred label: hasChecksum
has column label: checksum

has child
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range:
  union of: Donor
  union of: Family Member
  union of: HumanDonor
definition: A property that identifies genetic children.

has chromosome
type: DatatypeProperty
comment: Need definition
domain: SequenceLocation
range: string
preferred label: hasChromosome
has column label: chromosome

has clonality
type: DatatypeProperty
comment: Need definition
domain: Antibody
range: Datatype
  one of: monoclonal
  one of: polyclonal
has column label: clonality

has column label
type: AnnotationProperty
comment: Need definition
range: string

hasCountry
type: ObjectProperty
comment: Need definition

hasCrossReference
type: ObjectProperty
label: hasCellState
range:
  union of: anyURI
  union of: string
sub property of: closeMatch
definition: Reference to the entity in another electronic system. The data stored about the entity may vary from system to system, but this relationship asserts that the reference represents the same entity.
has column label: xref

hasCurrentAddress
type: ObjectProperty
comment: Need definition
domain: Organization
domain: Person
range: Address

hasDataModality
type: ObjectProperty
domain: Activity
domain: File
range: DataModality
definition: Data modality describes the biological nature of the information gathered as the result of an Activity, independent of the technology or methods used to produce the information.
has column label: data_modality

has date collected
type: Property
type: DatatypeProperty
domain: BioSample
domain: Measurement
range: dateTime
sub property of: date
definition: Date the BioSample was originally collected from its Donor.
has column label: date_collected

has date of birth
type: Property
type: DatatypeProperty
domain: Donor
domain: Family Member
range: dateTime
definition: A reference to the data of birth of the Donor or Family Member.
has column label: birth_date

has date of death
type: Property
type: DatatypeProperty
comment: Need definition
domain: Donor
domain: Family Member
range:
  union of: date
  union of: dateTime
sub property of: date

hasDevelopmentalStage
type: DatatypeProperty
comment: Need definition
domain: BioSample
range:
  union of: anyURI
  union of: string
has column label: developmental_stage

hasDiagnosis
type: ObjectProperty
domain: BioSample
domain: Family Member
domain: HumanDonor
range: Diagnosis
definition: A property that identifies a Diagnosis including provenance and the disease or condition diagnosed.
preferred label: has diagnosis
has column label: diagnosis_id

hasDisease
type: DatatypeProperty
domain: Resource
domain: BioSample
range:
  union of: OGMS_0000031
  union of: anyURI
definition: A property that identifies a disease or condition has been reported in this entity.
has column label: disease_id

disease stage type
type: DatatypeProperty
comment: Need definition
domain: Diagnosis
range:
  union of: anyURI
  union of: string
preferred label: has disease stage type
has column label: disease_stage_type

disease stage
type: DatatypeProperty
comment: Need definition
domain: Diagnosis
range: string
preferred label: has disease stage value
has column label: disease_stage_value

hasDonor
type: ObjectProperty
domain: BioSample
range: Donor
inverse of: donated
definition: This property references the Donor organism from which the BioSample was acquired.
has column label: donor

hasDonorAgeAtCollection
type: ObjectProperty
domain: BioSample
domain: Measurement
range: Age
definition: A reference to the Age of the Donor at the point in time that the BioSample was obtained or other representative entity (test, diagnosis, treatment...) was created.
has column label: donor_age_at_collection

hasDonorAgeAtEvent
type: ObjectProperty
domain: Activity
domain: Donor Treatment
range: Age
definition: A reference to the Age of the Donor at the point in time that the event or administration occured.
has column label: donor_age_at_event

has donor treatment type
type: DatatypeProperty
comment: Need to add recommended vocabulary.
domain: Donor Treatment
range: string
has column label: donor_treatment_type

has dose
type: DatatypeProperty
domain: Donor Treatment
definition: A reference to the dosage information relevant to this Donor Treatment or Medication.
has column label: dose

hasDuplicateFragments
type: DatatypeProperty
comment: For alignment data types.
comment: Need definition
domain: AlignmentFile
range: integer

has duration
type: DatatypeProperty
comment: Need definition
range: decimal
has column label: duration

has duration unit
type: DatatypeProperty
comment: Need definition
range: Datatype
  one of: min
  one of: seconds
  one of: hours
  one of: days
sub property of: hasUnit
has column label: duration_unit

hasEstimatedLibrarySize
type: DatatypeProperty
comment: For alignment file types.
comment: Need definition
domain: AlignmentFile
range: integer

hasFamilyIdentifier
type: DatatypeProperty
domain: Family Member
domain: HumanDonor
range: string
definition: A property identifies the family with whom this Donor is affiliated.
has column label: family_identifier

hasFileFormat
type: DatatypeProperty
comment: The definition of this field follows the convention used by the Human Cell Atlas.
domain: File
range: string
sub property of: format
definition: An indication of the format of an electronic file; include the full file extension including compression extensions.
has column label: file_format

hasFileSize
type: DatatypeProperty
domain: File
range: decimal
equivalent property: C171192
definition: Property that describes the approximate size of a file in megabytes.
has column label: file_size

hasFragments
type: DatatypeProperty
comment: For alignment file types.
comment: Need definition
domain: AlignmentFile
range: integer

hasGRCName
type: DatatypeProperty
comment: Name of the Reference Assembly in Genome Reference Consortium format (ncbi.nlm.nih.gov/grc. Still draft.
comment: Need definition
range: string

has gene context
type: DatatypeProperty
domain: SequenceLocation
range:
  union of: anyURI
  union of: string
definition: A specific gene identified that applies to this variant.
has column label: gene_context

hasGeneExpressionProgram
type: DatatypeProperty
domain: SingleCell
range:
  union of: anyURI
  union of: string
definition: A property that characterizes the gene expression patterns at work in the cell.
has column label: gene_expression_program

has genetic ancestry
type: DatatypeProperty
comment: Recommend using HANCESTRO ancestry category subclasses as options here.
domain: Family Member
domain: HumanDonor
range: anyURI
definition: A property that relects a HumanDonor's reported major contributing ancestral origins based on genetic/genomic data.
has column label: genetic_ancestry

has genetic modification
type: DatatypeProperty
domain: BioSample
range: string
definition: A reference to a genetic modification of a BioSample.
has column label: genetic_mod

has genetic modification method
type: DatatypeProperty
domain: BioSample
range: Datatype
  one of: CRISPR
  one of: mutagen treatment
  one of: site-specific recombination
  one of: TALEN
  one of: homologous recombination
definition: The method of a GeneticModification, see ValueSets.
has column label: genetic_mod_method

has genetic modification reference
type: DatatypeProperty
domain: BioSample
range: string
definition: An external reference to a genetic modification method.
has column label: genetic_mod_ref
range: anyURI

has genetic modification type
type: DatatypeProperty
comment: Need definition
domain: BioSample
range: Datatype
  one of: deletion
  one of: interference
  one of: insertion
  one of: mutagenesis
  one of: replacement
  one of: episome
  one of: activation
  one of: knockout
  one of: disruption
  one of: inhibition
  one of: binding
  one of: transgene insertion
  one of: deactivation
  one of: perturbation
  one of: selection
  one of: stimulation
  one of: non-specific target control
  one of: repression
  one of: tagging
  one of: characterization
  one of: expression
  one of: in vivo enhancer characterization
has column label: genetic_mod_type

hasGenotypicSex
type: DatatypeProperty
comment: Add equivalence to http://purl.obolibrary.org/obo/PATO_0020000
domain: BioSample
domain: Donor
domain: Family Member
range: string
definition: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. [PATO]
has column label: genotypic_sex

hasGrade
type: Property
range: string

hasHalfSibling
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range:
  union of: Family Member
  union of: HumanDonor
definition: A property that identifies genetic half siblings.
has column label: half_sibling

has host organism
type: DatatypeProperty
comment: Need definition
domain: Antibody
range:
  union of: OBI_0100026
  union of: string
has column label: host_organism

has immunogen
type: DatatypeProperty
comment: Need definition
comment: Target is a string for now but will ultimately be a class. CHEBI term CHEBI:60816
domain: Antibody
domain: Assay
domain: SampleTreatmentActivity
range:
  union of: anyURI
  union of: string
has column label: immunogen

hasLibraryLayout
type: DatatypeProperty
domain: Library
domain: SequenceFile
domain: Sequencing
range: Datatype
  one of: paired
  one of: single
definition: An indicator of whether the referenced library was prepared for paired or single end sequencing.
has column label: library_layout

hasLibraryPrep
type: ObjectProperty
comment: Need definition
domain: BioSample
range: LibraryPreparation
sub property of: wasUsedBy
definition: A subproperty of usedBy which indicates that LibraryPreparation was performed using this entity.
has column label: library_prep_id

hasLibraryPreparationType
type: ObjectProperty
comment: Need definition
domain: Library
domain: LibraryPreparation
range: OBI_0000711
has column label: library_prep_type

hasLifeStage
type: Property
comment: Need definition
comment: Varies per species; temporary solution
domain: Age
range: Datatype
  one of: embryonic
  one of: newborn
  one of: adolescent
  one of: adult
  one of: unknown
preferred label: has life stage
has column label: life_stage

hasLot
type: DatatypeProperty
comment: A serial or lot number that was manufactured together. Added for Antibodies but domain can expand.
domain: Antibody
range:
  union of: anyURI
  union of: string
definition: The lot unit of an entity.
has column label: lot

hasLowerBound
type: DatatypeProperty
comment: Need definition
domain: Age
domain: Weight
range: decimal
has column label: lower_bound

hasMailingAddress
type: Property
domain: Address
range: string
definition: Text form of the address, including country and postal code.
has column label: mailing_address

has manner of death
type: DatatypeProperty
comment: Need definition
domain: Family Member
domain: HumanDonor
range: string
has column label: manner_of_death

has measurement
type: ObjectProperty
domain: Donor
range: Measurement
definition: A reference to a Measurement related to this Donor.
has column label: measurement

has measurement type
type: DatatypeProperty
comment: Recommend LOINC or SNOMED vocabularies.
domain: Measurement
range:
  union of: anyURI
  union of: string
has column label: measurement_type

has medication
type: DatatypeProperty
comment: Recommend term or URL from MEDDRA or RxNORM. Note that this model of a medication is subject to change.
domain: Donor Treatment
range:
  union of: anyURI
  union of: string
definition: A reference to the medication information relevant to this entity.
has column label: medication

has missing value reason
type: AnnotationProperty
comment: The reason choices are taken from the International Nucleotide Sequencing Data Collaborative (INSDC); see https://www.insdc.org/missing-value-reporting#.
range: Datatype
  one of: not applicable
  one of: not collected
  one of: restricted
has column label: missing_value_reason

hasMolecularSampleType
type: ObjectProperty
domain: MolecularSample
range: MolecularSampleType
sub property of: hasSampleType
has column label: mol_sample_type

hasMorphology
type: DatatypeProperty
range: string
has column label: morphology

hasNonDuplicatedFragments
type: DatatypeProperty
comment: For alignment file types.
domain: SequenceFile
range: integer

hasOrganismType
type: Property
type: DatatypeProperty
comment: For example: Homo sapiens from NCBITaxon or http://purl.obolibrary.org/obo/NCBITaxon_9606
domain: Donor
domain: Family Member
range:
  union of: anyURI
  union of: string
definition: A reference to the organism type.
has column label: organism_type

hasPairedEndIdentifier
type: DatatypeProperty
range: Datatype
  one of: 1
  one of: 2

hasPairedNormal
type: Property
domain: BioSample
range: BioSample
has column label: paired_normal

hasPairedTumor
type: Property
domain: BioSample
range: BioSample
has column label: paired_tumor

hasParent
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range:
  union of: Family Member
  union of: HumanDonor
definition: A property that identifies genetic parents.
has column label: parent

has part number
type: DatatypeProperty
comment: The part number is for reordering. Added for Antibodies but domain can expand.
domain: Antibody
range: anyURI
definition: The part number or catalogue number (e.g. Stock Keeping Unit) of an entity.
has column label: part_number

hasPercentAlignedReads
type: DatatypeProperty
domain: SequenceFile
range: decimal

hasPercentDuplicateFragments
type: DatatypeProperty
comment: For alignment file types.
domain: SequenceFile
range: decimal

hasPhenopacket
type: ObjectProperty
domain: Diagnosis
range: File
definition: A reference to the phenopacket file.
has column label: phenopacket

hasPhenotype
type: DatatypeProperty
domain: Diagnosis
range: anyURI
definition: A reference to the phenotype, preferably from the Human Phenotype Ontology. Phenopackets handled separately.
has column label: phenotype

hasPhenotypeDescription
type: AnnotationProperty
domain: Diagnosis
range: string
definition: Phenotype term or free text description for additional phenotype information.
has column label: phenotype_description

hasPhenotypicSex
type: ObjectProperty
domain: Donor
range: Biological sex
equivalent property: PATO_0001894
definition: A reference to the BiologicalSex of the Donor organism. "An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. [PATO]"
has column label: phenotypic_sex

hasPlatform
type: Property
type: DatatypeProperty
domain: Activity
range:
  union of: anyURI
  union of: string
definition: A reference to the instrument or platform type used to conduct this activity.
preferred label: has platform
has column label: platform

hasPlatformID
type: Property
type: DatatypeProperty
domain: Activity
range:
  union of: anyURI
  union of: string
definition: A reference to the instrument or platform type used to conduct this activity.
preferred label: has platform identifier
has column label: platform_id

hasPostalCode
type: Property
domain: Address
range: string
has column label: post_code

hasPreservationState
type: DatatypeProperty
domain: BioSample
range: Datatype
  one of: Cryopreserved
  one of: FFPE
  one of: Fresh
  one of: Frozen
  one of: OCT-embedded
  one of: Snap Frozen
definition: Method used to preserve the BioSample, if relevant, or Fresh for BioSamples that were not preserved.
has column label: preservation_state

hasProtocol
type: DatatypeProperty
domain: Activity
range:
  union of: anyURI
  union of: string
sub property of: used
has column label: protocol

hasRace
type: DatatypeProperty
comment: Considering using HANCESTRO ancestry category subclasses as options here. In the meantime, capturing a text string. Also consider whether we need to track reported and genetic as determined by genetic analysis.
domain: Family Member
domain: HumanDonor
range: string
definition: A property that relects a HumanDonor's reported race.
preferred label: has race
has column label: race

hasReadCount
type: DatatypeProperty
comment: Domain will change from File to SequencingOutputFile or SequenceActivity in future.
domain: SequenceFile
range: integer

hasReadLength
type: DatatypeProperty
comment: Domain will change from File to SequencingOutputFile or SequenceActivity in future.
domain: SequenceFile
range: integer

hasReferenceAllele
type: DatatypeProperty
comment: See also https://vrs.ga4gh.org/en/stable/terms_and_model.html#allele for a more comprehensive model.
domain: VariantCall
range: string
definition: The state of a molecule at a identified location.
preferred label: has reference allele

has reported ethnicity
type: DatatypeProperty
comment: Recommend using HANCESTRO ancestry category subclasses but a text string is also acceptable.
domain: Family Member
domain: HumanDonor
range:
  union of: anyURI
  union of: string
definition: A property that relects a HumanDonor's reported ethnic origins.
has column label: reported_ethnicity

has sample treatment
type: ObjectProperty
domain: BioSample
range: SampleTreatmentActivity
sub property of: wasUsedBy
definition: A subproperty of prov:usedBy which indicates that a SampleTreatmentActivity was performed using this entity.
definition: A sample treatment of a BioSample.
has column label: sample_treatment_id

has sample treatment method
type: DatatypeProperty
domain: SampleTreatmentActivity
range: string
definition: The method of a SampleTreatmentActivity.
has column label: sample_treatment_method

has sample treatment type
type: DatatypeProperty
domain: SampleTreatmentActivity
range: Datatype
  one of: antibody
  one of: chemical
  one of: exposure
  one of: infection
  one of: injection
  one of: irradiation
  one of: protein
  one of: transplantation
  one of: RNAi
  one of: CRISPRi
definition: The type of a BioSample treatment type, see valuesets for examples.
has column label: sample_treatment_type

hasSampleType
type: DatatypeProperty
domain: Sample
has column label: sample_type

hasSequenceExpression
type: DatatypeProperty
comment: See https://vrs.ga4gh.org/en/stable/terms_and_model.html#sequence-expression and https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/index.html#expression.
domain: VariantCall
range: string
definition: An expression describing a Sequence, for example HGVS or ISCN.
preferred label: has sequence expression
has column label: sequence_expression

hasSequenceLocation
type: ObjectProperty
definition: Location of variation on a sequence. For example, for human genome: chr7:140753336-140753337
domain: VariantCall
range:
  union of: string
  union of: SequenceLocation
alternative label: hasLocation
has column label: seq_location

hasSequencing
type: ObjectProperty
domain: BioSample
range: Sequencing
sub property of: wasUsedBy
definition: A subproperty of usedBy which indicates that a SequencingActivity was performed using this entity.

has service provider
type: Property
type: ObjectProperty
domain: Activity
range:
  union of: string
  union of: Organization
definition: A reference to the organization performing this activity.
has column label: service_provider

hasSexAssignedAtBirth
type: ObjectProperty
domain: Donor
range: Biological sex
definition: A reference to the BiologicalSex assigned to the donor organism at birth by a medical professional.
has column label: sex_assigned_at_birth

hasSibling
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range:
  union of: Family Member
  union of: HumanDonor
definition: A property that identifies full genetic siblings.
has column label: sibling

hasSource
type: DatatypeProperty
comment: The source is a string but will ultimately be a Vendor class. Added for Antibodies but domain can expand.
domain: Antibody
range:
  union of: anyURI
  union of: string
definition: The source of production for an entity.
has column label: source

hasStage
type: Property
range: string

hasStartPosition
type: DatatypeProperty
domain: SequenceLocation
range: integer
definition: A reference to the start position on the chromosome identified.
has column label: start_position

hasStopPosition
type: DatatypeProperty
domain: SequenceLocation
range: integer
has column label: stop_position

hasStrain
type: DatatypeProperty
domain: Resource
domain: DogDonor
domain: Donor
domain: MouseDonor
range: string
definition: Text string to represent the strain.

hasVariantReference
type: DatatypeProperty
domain: VariantCall
range:
  union of: anyURI
  union of: string
definition: A sequence variant that changes one or more structural features. (Sequence Ontology)

hasTarget
type: DatatypeProperty
comment: Need definition
comment: Target is a string for now but will ultimately be a class, and this will change to an ObjectProperty.
domain: Antibody
domain: Assay
domain: SampleTreatmentActivity
range:
  union of: anyURI
  union of: string
has column label: target

has temperature
type: Property
comment: Need definition
range: decimal
has column label: temperature

has temperature unit
type: DatatypeProperty
comment: Need definition
range: Datatype
  one of: celsius
  one of: kelvin
  one of: fahrenheit
sub property of: hasUnit
has column label: temperature_unit

hasTermName
type: DatatypeProperty
domain: OntologyReference
range: string

hasTreatment
type: ObjectProperty
domain: Diagnosis
domain: Donor
domain: HumanDonor
range: Donor Treatment
definition: A reference to the therapeutic treatment undertaken for this Donor.
preferred label: has treatment
has column label: treatment_id

has treatment outcome
type: Property
type: DatatypeProperty
comment: Should the model define a preferred vocabulary? e.g. positive, negative, no effect? The specific outcome may need to be more specific, reduced tumor size by .. but the categories listed are useful.
domain: Donor Treatment
range: string
definition: A reference to the outcome of this Treatment.
has column label: treatment_outcome

hasTumorMorphology
type: DatatypeProperty
comment: Need definition
range: string
sub property of: hasMorphology

hasURI
type: DatatypeProperty
comment: Need definition
domain: anyURI
range: anyURI

hasUnit
type: DatatypeProperty
comment: Need definition
range: string

hasUpperBound
type: DatatypeProperty
comment: Need definition
domain: Age
domain: Weight
range: decimal

hasVariantCall
type: ObjectProperty
comment: Need definition
domain: VariantCallSet
range: VariantCall

hasVersion
type: DatatypeProperty
comment: Need definition
domain: File
range: string

hasWeight
type: ObjectProperty
domain: BFO_0000040
range: Weight
definition: A property that provides a measurement of the mass of a material entity.

hasWeightUnit
type: DatatypeProperty
domain: Weight
range: Datatype
  one of: lbs
  one of: kg
sub property of: hasUnit
definition: A reference to the measurement unit for mass.

id
type: Property
comment: Need definition
domain: Entity
range:
  union of: anyURI
  union of: string
sub property of: identifier

cause of death
type: DatatypeProperty
comment: Need definition
domain: Diagnosis
range: boolean
has column label: cause_of_death

contributes to death
type: DatatypeProperty
comment: Need definition
domain: Diagnosis
range: boolean
has column label: contributor_to_death

isFundedBy
type: ObjectProperty
rdf-schema#: Project
range: Organization
definition: A relationship defining the funding source. The range is expected to include grants, organizations, or a string indicating the funding source.
has column label: funded_by

isGeneratedByPipeline
type: ObjectProperty
comment: Need definition
range: Analysis
sub property of: wasGeneratedBy

isPairedWith
type: ObjectProperty
comment: Need definition
domain: Library
domain: SequenceFile
range:
  union of: Library
  union of: SequenceFile
has column label: paired_with

isWholeCell
type: DatatypeProperty
comment: Need definition
domain: SingleCell
range: boolean

usesAntibody
type: ObjectProperty
comment: Can be used as an ObjectProperty with the Antibody class or as a DataType property, depending on need. Antibody should be linked to OBI in future. Note this could link to nonassay activities like CHiP
domain: OBI_0001954
domain: Activity
domain: Assay
range:
  union of: string
  union of: Antibody
sub property of: used
definition: May be a reference to an antibody used for a SampleTreatmentActivity or another Activity.
has column label: antibody

usesLibrary
type: ObjectProperty
domain: Assay
domain: SequenceFile
domain: Sequencing
range: Library
sub property of: used
definition: A reference to a Sequencing Library used in this activity.
has column label: library

usesReferenceAssembly
type: ObjectProperty
domain: Alignment
domain: AlignmentFile
domain: SequenceFile
domain: Sequencing
domain: VariantCall
domain: VariantCallingActivity
range:
  union of: anyURI
  union of: string
  union of: ReferenceAssembly
definition: A reference to the collection of sequences taken as the standard for a given organism. May be defined by https://www.ncbi.nlm.nih.gov/grc.
has column label: uses_reference_assembly

usesSample
type: ObjectProperty
comment: BioSample and MolecularSample both inherit range from Sample
range: Sample
sub property of: used
definition: A reference to the sample used by this activity.
has column label: uses_sample

uses software
type: DatatypeProperty
domain: Analysis
range:
  union of: anyURI
  union of: string
definition: A reference to a software tool or command line
has column label: uses_software

DataCollection
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: hasCustodian

DataSnapshot
subclass of: Restriction
  cardinality: 1
  on property: identifier
subclass of: Restriction
  cardinality: 1
  on property: id

Dataset
subclass of: Restriction
  cardinality: 1
  on property: description
subclass of: Restriction
  cardinality: 1
  on property: title
subclass of: Restriction
  cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 1
  on property: contactPoint
subclass of: Restriction
  min cardinality: 1
  on property: hasDataModality
subclass of: Restriction
  min cardinality: 1
  on property: hasCustodian
subclass of: Restriction
  min cardinality: 1
  on property: hasDataUsePermission
subclass of: Restriction
  min cardinality: 1
  on property: hasOwner

hasConsentGroup
has column label: consent_group

hasDataUseModifier
has column label: data_use_modifier

hasDataUsePermission
has column label: data_use_permission

hasOriginalPublication
has column label: original_publication

hasOwner
has column label: owner

hasPrincipalInvestigator
range:
  union of: string
  union of: Principal Investigator
has column label: principal_investigator

hasRegisteredIdentifier
has column label: registered_id