contributor
has column label: contributor

description
has column label: description

license
has column label: license

title
has column label: title

endedAtTime
has column label: end_time

generated
has column label: generated

contactPoint
has column label: contact_point

hadDerivation
type: ObjectProperty
inverse of: wasDerivedFrom
definition: Inverse of prov:wasDerivedFrom

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: owl
imports: EFO subset
imports: NCBITaxon Organisms subset
imports: OBI assaySubset
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
  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: 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: 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: AlignmentPostProcessing
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Pipeline
disjoint with: Sequencing
disjoint with: VariantCalling
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: usesReferenceAssembly
subclass of: Restriction
  max cardinality: 1
  on property: hasPercentAlignedReads
definition: An electronic record of the alignment of a genetic sequence for a particular Sample compared with a reference sequence generated by an AlignmentActivity.

AlignmentPostProcessing
type: Class
subclass of: Pipeline
subclass of: Restriction
  on property: generated
  some values from: AlignmentFile
subclass of: Restriction
  on property: used
  some values from: AlignmentFile
disjoint with: Alignment
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Sequencing
disjoint with: VariantCalling
definition: An activity that further processed the output of an Alignment Activity on a genetic sequence.

Antibody
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  cardinality: 1
  on property: hasHostOrganism
subclass of: Restriction
  min cardinality: 1
  on property: hasClonality
subclass of: Restriction
  min cardinality: 1
  on property: hasTarget

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

BioSample
type: Class
subclass of: Sample
subclass of: Restriction
  all values from: Datatype
    one of: primary
    one of: metastatic
  on property: hasPrimaryOrMetastaticIndicator
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: 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: hasDonorAgeAtCollection
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
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.

ChromosomalLocation
type: Class
subclass of: SequenceLocation
subclass of: Restriction
  cardinality: 1
  on property: hasChromosome
definition: The location of a sequence feature defined by its start and end position on a chromosome in a reference coordinate system.

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
definition: Result of a medical investigation that often identies a disease or condition.

Dog
type: NCBITaxon 9615

DogDonor
type: Class
subclass of: Donor
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: identifier
subclass of: Restriction
  cardinality: 1
  on property: hasOrganismType
subclass of: Restriction
  max cardinality: 1
  on property: hasAge
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: hasCrossReference
subclass of: Restriction
  min cardinality: 1
  on property: has BioSample
subclass of: Restriction
  on property: isPartOf
  some values from: Dataset
definition: An organism from which a sample or test result is available

Family Member
type: Class
subclass of: OBI_0100026
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
  min cardinality: 0
  on property: has genetic ancestry
subclass of: Restriction
  min cardinality: 0
  on property: has genetic ancestry
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
  min cardinality: 0
  on property: hasChecksum
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
  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
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
  has value: Human
  on property: hasOrganismType
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
  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
  max cardinality: 1
  on property: hasLibraryPreparationType
subclass of: Restriction
  on property: generated
  some values from: Library
disjoint with: Alignment
disjoint with: AlignmentPostProcessing
disjoint with: Assay
disjoint with: Pipeline
disjoint with: Sequencing
disjoint with: VariantCalling
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

MedicalHistory
type: Class
subclass of: IAO_0000030
definition: Placeholder for medical record information. Likely a series of visits/encounters with results. Need to connect to the BioSample.

MolecularSample
type: Class
subclass of: Sample
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
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
equivalent class: EFO_0007831
definition: Activity to separate the nucleus or nuclei from the cell.

OntologyReference
type: Class
subclass of: IAO_0000027

Pipeline
type: Class
subclass of: Activity
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: AlignmentPostProcessing
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Sequencing
disjoint with: VariantCalling
definition: An activity that records the output of a specific software pipeline. Pipeline version, components, arguments are described in prov:SoftwareAgent.

Principal Investigator
type: Class
subclass of: Person
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: title
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
  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: hasDataUsePermission
subclass of: Restriction
  max cardinality: 1
  on property: created
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.

SequenceFile
type: Class
subclass of: File
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
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: hasLocation
subclass of: Restriction
  cardinality: 1
  on property: hasStartPosition
subclass of: Restriction
  cardinality: 1
  on property: hasStopPosition
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
  min cardinality: 1
  on property: usesSample
subclass of: Restriction
  on property: generated
  some values from: SequenceFile
disjoint with: Alignment
disjoint with: AlignmentPostProcessing
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Pipeline
disjoint with: VariantCalling
definition: An activity that produces an electronic record of a genetic sequence from a Sample

SingleCell
type: Class
subclass of: BioSample
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
definition: An activity that infers a cell type based on analysis.

SingleCellIsolation
type: Class
subclass of: Activity
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
  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
  min cardinality: 0
  on property: hasVariantCall
definition: An electronic record of a collection of variations in genetic sequence for a particular Sample that have been generated by a VariantCallingActivity.

VariantCalling
type: Class
subclass of: Activity
subclass of: Restriction
  min cardinality: 1
  on property: usesReferenceAssembly
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: AlignmentPostProcessing
disjoint with: Assay
disjoint with: LibraryPreparation
disjoint with: Pipeline
disjoint with: Sequencing
definition: An activity that identifies genetic sequence alterations in a Sample when compared to a reference.

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: OGMS_0000031
range: OntologyReference
definition: A property that identifies a disease or condition has been confirmed through diagnosis. Contrast with hasDisease.
has column label: disease

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.

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
domain: File
range: integer

hasAllele
type: DatatypeProperty
domain: VariantCall
range: string

hasAlpha2Code
type: AnnotationProperty
domain: Country
range: string

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: anyURI
range: string
definition: A reference to the physical location within the AnatomicalSite from which the BioSample was taken.

hasAnatomicalSite
type: DatatypeProperty
comment: May want to consider restricting this to UBERON terms but currently any URI is allowed.
domain: BioSample
range: anyURI
definition: A reference to the site within the organism from which the BioSample was taken.
has column label: anatomical_site

hasAprioriCellType
type: ObjectProperty
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: ObjectProperty
domain: Assay
range: OBI_0000070
has column label: assay_type

hasAverageReadLength
type: DatatypeProperty
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
domain: BioSample
range: BioSampleType
sub property of: hasSampleType
has column label: biosample_type

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

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

hasCellState
type: DatatypeProperty
domain: SingleCell
range: anyURI
range: string
definition: A property that describes the cell’s metabolic or electrophysiological state.

hasChecksum
type: DatatypeProperty
domain: File
range: string
has column label: checksum

hasChild
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range: Family Member
range: HumanDonor
definition: A property that identifies genetic children.

hasChromosome
type: DatatypeProperty
domain: ChromosomalLocation
range: string
has column label: chromosome

hasClonality
type: DatatypeProperty
domain: Antibody
range: Datatype
  one of: monoclonal
  one of: polyclonal

has column label
type: AnnotationProperty
range: string

hasCountry
type: ObjectProperty

hasCrossReference
type: ObjectProperty
range: anyURI
range: 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
domain: Organization
domain: Person
range: Address

hasDataModality
type: ObjectProperty
domain: Activity
domain: File
range: DataModality
has column label: data_modality

has date collected
type: Property
type: DatatypeProperty
domain: BioSample
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
domain: Donor
domain: Family Member
range: date
range: dateTime
sub property of: date

hasDevelopmentalStage
type: ObjectProperty
domain: BioSample
range: anyURI
range: string

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

hasDisease
type: DatatypeProperty
domain: Resource
domain: BioSample
range: OGMS_0000031
range: OntologyReference
definition: A property that identifies a disease or condition has been reported in this entity.

disease stage type
type: DatatypeProperty
domain: Diagnosis
range: URI
range: string
preferred label: has disease stage type
has column label: disease_stage_type

disease stage
type: DatatypeProperty
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.

hasDonorAgeAtCollection
type: ObjectProperty
domain: BioSample
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

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

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

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

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.
domain: AlignmentFile
domain: File
range: integer

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

hasGeneExpressionProgram
type: DatatypeProperty
domain: SingleCell
range: anyURI
range: string
definition: A property that characterizes the gene expression patterns at work in the cell.

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

hasGenotypicSex
type: string
comment: Add equivalence to http://purl.obolibrary.org/obo/PATO_0020000
domain: Donor
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: Family Member
range: HumanDonor
definition: A property that identifies genetic half siblings.
has column label: half_sibling

hasLibraryLayout
type: DatatypeProperty
domain: Library
domain: SequenceFile
range: Datatype
  one of: paired
  one of: single
has column label: library_layout

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

hasLibraryPreparationType
type: ObjectProperty
domain: Library
domain: LibraryPreparation
range: OBI_0000711

hasLocation
type: DatatypeProperty
comment: Location of variation on a sequence. For example, for human genome: chr7:140753336-140753337
domain: SequenceLocation
range: string

hasLowerBound
type: DatatypeProperty
domain: Age
domain: Weight
range: decimal

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

has manner of death
type: ObjectProperty
domain: Family Member
domain: HumanDonor
range: string

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

hasMorphology
type: ObjectProperty
range: string

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

hasOrganismType
type: ObjectProperty
comment: For example: Homo sapiens from obo:NCBITaxon_9606
domain: Donor
range: OBI_0100026
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

hasPairedTumor
type: Property
domain: BioSample
range: BioSample

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

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

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

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

hasPostalCode
type: Property
domain: Address
range: string

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

hasPrimaryOrMetastaticIndicator
type: DatatypeProperty
domain: BioSample
range: string

hasProtocol
type: DatatypeProperty
domain: Activity
range: anyURI
range: 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

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: anyURI
range: string
definition: A property that relects a HumanDonor's reported ethnic origins.
has column label: reported_ethnicity

hasSampleType
type: ObjectProperty
domain: Sample

hasSequenceLocation
type: ObjectProperty
domain: VariantCall
range: SequenceLocation

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.

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: Family Member
range: HumanDonor
definition: A property that identifies full genetic siblings.
has column label: sibling

hasStage
type: Property
range: string

hasStartPosition
type: DatatypeProperty
domain: SequenceLocation
range: integer
has column label: start_position

hasStopPosition
type: DatatypeProperty
domain: SequenceLocation
range: integer

hasStrain
type: DatatypeProperty
domain: Resource
domain: Donor
range: string
definition: Text string to represent the strain of the donor organism.

hasTarget
type: DatatypeProperty
comment: Target is a string for now but will ultimately be a class.
domain: Antibody
domain: Assay
range: anyURI

hasTermName
type: DatatypeProperty
domain: OntologyReference
range: string

hasTumorMorphology
type: ObjectProperty
range: string
sub property of: hasMorphology

hasURI
type: DatatypeProperty
domain: OntologyReference
range: anyURI

hasUnit
type: DatatypeProperty

hasUpperBound
type: DatatypeProperty
domain: Age
domain: Weight
range: decimal

hasVariantCall
type: ObjectProperty
domain: VariantCallSet
range: VariantCall

hasVariantReference
type: ObjectProperty
domain: VariantCall
range: string
sub property of: relatedMatch

hasVersion
type: DatatypeProperty
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.

cause of death
type: DatatypeProperty
domain: Diagnosis
range: boolean

contributes to death
type: ObjectProperty
domain: Diagnosis
range: boolean

isFundedBy
type: ObjectProperty
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
range: Pipeline
sub property of: wasGeneratedBy

isPairedWith
type: ObjectProperty
domain: Library
domain: SequenceFile
range: Library
range: SequenceFile

isWholeCell
type: DatatypeProperty
domain: SingleCell
range: boolean

usesAntibody
type: ObjectProperty
comment: Antibody should be linked to OBI in future.
domain: OBI_0001954
domain: Assay
range: Antibody
sub property of: used

usesLibrary
type: ObjectProperty
domain: Assay
domain: SequenceFile
domain: Sequencing
range: Library
sub property of: used
has column label: library

usesReferenceAssembly
type: ObjectProperty
comment: Still in draft
domain: Alignment
domain: AlignmentFile
domain: SequenceFile
domain: Sequencing
range: ReferenceAssembly
sub property of: used
has column label: reference_assembly

usesSample
type: ObjectProperty
range: BioSample
sub property of: used
has column label: sample

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

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

Dataset
subclass of: Restriction
  min cardinality: 1
  on property: hasCustodian

hasDataUseModifier
has column label: data_use_ modifier

hasDataUsePermission
has column label: data_use_permission

hasOriginalPublication
has column label: original_plublication

hasPrincipalInvestigator
range: Principal Investigator
has column label: principle_investigator