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Donor Schema

The BICAN Donor Metadata schema specifies the metadata relating to donors in BICAN. These metadata reflect the metadata needed to accurately track donors and related entities from the brain banks through the specimen portal.

URI: https://w3id.org/brain-bican/donor

Name: Donor

Classes

Class Description
Annotation Biolink Model root class for entity annotations
        QuantityValue A value of an attribute that is quantitative and measurable, expressed as a c...
ChemicalEntityOrGeneOrGeneProduct A union of chemical entities and children, and gene or gene product
Entity Root Biolink Model class for all things and informational relationships, real...
        NamedThing a databased entity or concept/class
                Activity An activity is something that occurs over a period of time and acts upon or w...
                Attribute A property or characteristic of an entity
                BiologicalEntity
                        Gene A region (or regions) that includes all of the sequence elements necessary to...
                        Genome A genome is the sum of genetic material within a cell or virion
                InformationContentEntity a piece of information that typically describes some topic of discourse or is...
                        Dataset an item that refers to a collection of data from a data source
                        StudyResult A collection of data items from a study that are about a particular study sub...
                                RelativeFrequencyAnalysisResult A result of a relative frequency analysis
                OrganismTaxon A classification of a set of organisms
                PhysicalEntity An entity that has material reality (a
                        Donor A person or organism that is the source of a biological sample for scientific...
                        MaterialSample A sample is a limited quantity of something (e
                Procedure A series of actions conducted in a certain order or manner
GenomicEntity
MacromolecularMachineMixin A union of gene locus, gene product, and macromolecular complex
        GeneOrGeneProduct A union of gene loci or gene products
OntologyClass a concept or class in an ontology, vocabulary or thesaurus
        TaxonomicRank A descriptor for the rank within a taxonomic classification
PhysicalEssenceOrOccurrent Either a physical or processual entity
        Occurrent A processual entity
                ActivityAndBehavior Activity or behavior of any independent integral living, organization or mech...
        PhysicalEssence Semantic mixin concept
ProvActivity An activity is something that occurs over a period of time and acts upon or w...
ProvEntity An entity is a physical, digital, conceptual, or other kind of thing with som...
SubjectOfInvestigation An entity that has the role of being studied in an investigation, study, or e...
ThingWithTaxon A mixin that can be used on any entity that can be taxonomically classified

Slots

Slot Description
age_at_death_reference_point Reference point from which the donor's age at death was calculated
age_at_death_unit The unit of the value mentioned under "age_at_death_value"
age_at_death_value Donor's age at death value
age_of_death Donor's age at death in years
aging_type The type of aging-related neuropathology diagnosis
antemortem_mri_available Is an Antemortem MRI is available?
apgar_10_minute_score The APGAR Ten Minute Score
apgar_5_minute_score The APGAR Five Minute Score
artifacts_type The type of artifacts
attribute_name The human-readable 'attribute name' can be set to a string which reflects its...
birth_country_name Donor's birth country
birth_weight_lbs Birth weight in pounds
birth_weight_oz Birth weight in ounces
brain_weight The weight of the brain in grams
category Name of the high level ontology class in which this entity is categorized
chembl_chirality Tern indicating the chirality of the chemical entity
chembl_drug_warning Text describing warnings for use of chemicals as therapeutics
chembl_prodrug Flag indicating if a drug is a prodrug that is active only after being metabo...
clinical_brain_diagnosis The ICD-10 code of the clinical brain diagnosis
clinical_brain_diagnosis_confidence_level The confidence level of the clinical brain diagnosis
confirmed_hbcac Confirmation status of meeting inclusion criteria of the Human Brain Cell Atl...
consent_status Whether the type of consent is open or controlled
creation_date date on which an entity was created
death_causes_data_available NIMP indicator for availability of the cause of death
deprecated A boolean flag indicating that an entity is no longer considered current or v...
description a human-readable description of an entity
developmental_type_specify The developmental neuropathology diagnoses specified
donor_labs Donor Labs
donor_project Donor Project
donor_source The source of the donor brain e
donor_species NCBI Taxonomy code of the donor species
education_years_number Number of years of education the donor had
equivalent_identifiers A set of identifiers that are considered equivalent to the primary identifier...
ethnicity Ethnicity of the donor
exact_match An external concept that is interchangeable with this entity
format
full_name a long-form human readable name for a thing
gender Donor's gender at death
genetic_diagnosis_code The ICD-10 code of the genetic diagnosis
genetic_diagnosis_confidence_level The confidence level of the genetic diagnosis
handedness Donor's handedness
has_attribute connects any entity to an attribute
has_attribute_type connects an attribute to a class that describes it
has_biological_sequence connects a genomic feature to its sequence
has_numeric_value connects a quantity value to a number
has_qualitative_value connects an attribute to a value
has_quantitative_value connects an attribute to a value
has_taxonomic_rank
has_unit connects a quantity value to a unit
hemisphere Hemisphere of the brain
id A unique identifier for an entity
in_taxon connects an entity to its taxonomic classification
in_taxon_label The human readable scientific name for the taxon of the entity
infectious_testings_data_available NIMP indicator for availability of infectious Disease/Serology testing data
infectious_type_specify The infectious neuropathology diagnoses specified
inflammatory_type_specify The inflammatory neuropathology diagnoses specified
information_content Information content (IC) value for a term, primarily from Automats
iri An IRI for an entity
left_hemisphere_prep_2 The second method used to prepare the left hemisphere
left_hemisphere_preparation The method of which the left hemisphere of the brain was prepared
license
macromolecular_machine_mixin_name genes are typically designated by a short symbol and a full name
marital_status Donor's marital or partner status
name A human-readable name for an attribute or entity
named_thing_category Name of the high level ontology class in which this entity is categorized
neoplastic_type The type of neoplastic neuropathology diagnosis
neurodegenerative_type The type of neurodegenerative neuropathology diagnosis
neurologic_events_data_available NIMP indicator for availability of perinatal neurologic events data
neuropathology_diagnosis_code The ICD-10 codes for the neuropathological diagnoses
nn_diagnoses_data_available NIMP indicator for availability of non-neuropathological diagnoses data
node_property A grouping for any property that holds between a node and a value
non_brain_diagnosis_code The ICD-10 code of the non-brain diagnosis
non_brain_diagnosis_confidence_level The confidence level of the non-brain diagnosis
non_brain_specimen_data_available NIMP indicator for availability of non-brain Specimen data
non_brain_tissue_available Are any non-brain tissues available?
organism_taxon_has_taxonomic_rank
ph pH value
photo_2d_available Is a 2D photograph is available?
positive_test_result Whether the donor has had a positive serology test result
post_mortem_interval Post Mortem Interval in hours
postmortem_mri_available Is a Postmortem MRI Available
postmortem_mri_type The type of postmortem MRI if it is available
primary_language Donor's primary language
provided_by The value in this node property represents the knowledge provider that create...
race Race of the donor
related_to A relationship that is asserted between two named things
related_to_at_instance_level Represents a relationship held between two instances of a data classes
repository If the brain is from NBB the NBB repository the brain belongs to
right_hemisphere_prep_2 The second method used to prepare the right hemisphere
right_hemisphere_preparation The method of which the right hemisphere of the brain was prepared
rights
rin RNA Integrity Number
rine RNA Integrity Number equivalent
rines_data_available NIMP indicator for availability of RNA Integrity Number equivalent
rins_data_available NIMP indicator for availability of RNA Integrity Number
scan_3d_available Is a 3D scan is available?
secondary_language Donor's secondary language
secondary_race Second race if available for the donor
sex Donor's sex at birth
sex_orientation Donor's sexual orientation at death
symbol Symbol for a particular thing
synonym Alternate human-readable names for a thing
tissue_type The type of non-brain tissues
tox_screening_data_available NIMP indicator for availability of toxicology screening data
traumatic_type The type of traumatic neuropathology diagnosis
type
used Usage is the beginning of utilizing an entity by an activity
vascular_type The type of vascular neuropathology diagnosis
version
was_derived_from A derivation is a transformation of an entity into another, an update of an e...
was_generated_by Generation is the completion of production of a new entity by an activity
weighed_type The type of the brain tissue weighed based on the preparation
xref A database cross reference or alternative identifier for a NamedThing or edge...

Enumerations

Enumeration Description
AgingType
ArtifactType
BirthCountry Namibia
BrainTissueWeightType
CauseOfDeath
ConditionType
ConfidenceLevel
DonorSource
DrugsFound
Ethnicity
Gender
Handedness
Hemisphere
IncomeRange
InformantRelationship
Language
MannerOfDeath
MaritalStatus
NeoplasticType
NeurodegenerativeType
PerinatalEvent
PostmortemMRI
Preparation
Race
RelativeType
Repository
Sex
SexualOrientation
TestName
Tissue
TissueCollectionState
TissueSource
TraumaticType
VascularType

Types

Type Description
BiologicalSequence
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
IriType An IRI
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
LabelType A string that provides a human-readable name for an entity
NarrativeText A string that provides a human-readable description of something
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
SymbolType
Time A time object represents a (local) time of day, independent of any particular...
Unit
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description
ModelOrganismDatabase Subset that is relevant for a typical Model Organism Database (MOD)
Restricted The data stored in this attribute is restricted to people with a required cle...
Samples Sample/biosample datamodel
Testing TBD
TranslatorMinimal Minimum subset of translator work