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ACR Harmonized Data Model

LinkML Schema for ACR Harmonized Data.

URI: https://anvilproject.org/acr-harmonized-data-model

Name: acr-harmonized-data-model

Classes

Class Description
Thing Highest Level Class
        AccessControlledRecord Element for which specific access control restrictions apply
                Aliquot Specific tubes or details of a Sample
                BiospecimenCollection Biospecimen Collection
                Demographics Basic participant demographics summary
                Family A group of individuals of some relation who are grouped together in the study
                FamilyMember Designates a Subject as a member of a family with some specified role
                FamilyRelationship A relationship between two Subjects
                File File
                Sample Biospecimen data
                SourceData Reference to submitted data used to generate harmonized data
                Subject This entity is the subject about which data or references are recorded
                SubjectAssertion Assertion about a particular Subject
        AccessPolicy Describes the access required for a given element of data
        DataSource Query configuration for specifying a source from which data are pulled
        FileMetadata Metadata about the contents of the file
        Study Study Meta Data

Slots

Slot Description
access_policy_code Access Policy Code
age_at_assertion The age in decimal years of the Subject when the assertion was made
age_at_collection The age at which this biospecimen was collected
age_at_event The age in decimal years of the Subject at the time point which the assertion...
age_at_last_vital_status Age at last vital status in decimal years
age_at_resolution The age in decimal years of the Subject when the asserted state was resolved
aliquots Aliquot(s) from this Sample
assertion_type The semantic type of the resource, eg, Condition
availablity_status Can this Sample be requested for further analysis?
biospecimen_collection Biospecimen Collection that generated this sample
code The structured term defining the meaning of the assertion
concentration_number What is the concentration of the analyte in the Aliquot?
concentration_unit Units associated with the concentration of the analyte in the Aliquot? UCUM c...
consanguinity Is there known or suspected consanguinity in this study family?
data_access_type Data Access Type
data_source Defines the location of data and how to query it
data_type The type of data within this file
date_of_birth Date at which the individual was born
date_of_birth_type Privacy rule modification applied to date_of_birth
description Description
disease_limitation Disease Use Limitations
display The friendly display string of the coded term
drs_uri DRS location to access the data
ethnicity Reported ethnicity as defined by the 1997 OMB directives
ethnicity_display The friendly display string of the coded term for Ethnicity
external_id Other identifiers for this entity, eg, from the submitting study or in system...
external_study_id External Study ID
family_description Free title describing the study family, such as potential inheritance or deta...
family_member The family member Subject who is the relationship "subject"
family_members The Subjects who are included in this family and their roles
family_relationships Family relationships associated with this family
family_role The "role" of this individual in this family
family_study_focus What is this study family investigating? EG, a specific condition
family_type Describes the 'type' of study family, eg, trio
file_metadata Additional metadata about the contents of the file, eg, genome reference buil...
filename The name of the file
format The format of the file
funding_source Funding Source
google_data_project The Google Data Project needed to query this snapshot in BigQuery
has_access_policy Which access policy applies to this element?
has_assertion Which assertions are made about this Subject?
has_demographics A demographic summary of the participant
has_sample Which samples were collected or processed for this Subject?
id ID associated with a class
in_study With which study is this class associated?
laterality Laterality information for the site
method The approach used to collect the biospecimen
organism_type Organism Type Label
other_family_member The family member Subject for the relationship "object"
parameterized_query A parameterized query that contains the primary key fields and can be used to...
parent_sample Sample from which this sample is derived
parent_study_id Parent Study ID
principal_investigator Principal Investigator
processing Processing that was applied to the Parent Sample or from the Biospecimen Coll...
quantity_number The total quantity of the specimen
quantity_units The structured term defining the units of the quantity
query_parameter One or more query parameters used to select the specific row
race Reported race as defined by the 1997 OMB directives
race_display The friendly display string of the coded term(s) for Race
relationship_code Code definting the relationship predicate
sample The Samples(s) used to generate data in this file
sample_type Type of material of which this Sample is comprised
sex Sex of the individual
sex_display The friendly display string of the coded term for Sex
site The location of the specimen collection
size Size of the file, in Bytes
snapshot_dataset The Dataset within BigQuery where the table can be queried
snapshot_id The Terra Data Repository Snapshot ID
source_data The sources from which this assertion was derived
spatial_qualifier Any spatial/location qualifiers
storage_method Sample storage method, eg, Frozen or with additives
study_title Study Title
subject The Subject(s) which this file describes
subject_type Type of entity this record represents
table The table in the dataset that contains the row of interest
value_code The structured term defining the value of the assertion
value_display The friendly display string of the coded term for the value of the assertion
value_number The numeric value of the assertion
value_units The structured term defining the units of the value
value_units_display The friendly display string of units of the value
vital_status Vital Status
website Website

Enumerations

Enumeration Description
EDAMDataTypes Data types from the EDAM ontology
EDAMFormats Data formats from the EDAM ontology
EnumAccessCode Type of research use case allowed
EnumAccessType Type of access controls applied
EnumAssertionType Provides options to describe the expressed semantics of a condition
EnumAvailabilityStatus Is the Thing available for use?
EnumConditionAssertion Enumerations for Condition Assertion
EnumConditionCode Recommended ontologies include: SNOMED_CT, HP, OMIM and ORPHA, prefixed with ...
EnumConsanguinityAssertion Asserts known or suspected consanguinity in this study family
EnumDateOfBirthType Privacy rules that may modify a date value
EnumEthnicity OMB Codes describing Hispanic or Latino ethnicity
EnumFamilyType Enumerations describing research family type
EnumLaterality Laterality information for the site
EnumRace OMB Codes describing race
EnumSampleCollectionMethod The approach used to collect the biospecimen
EnumSex Terms describing an individual's sex
EnumSite The location of the specimen collection
EnumSpatialQualifiers Any spatial/location qualifiers
EnumSubjectType Types of entities
EnumVitalStatus Is the entity living?

Types

Type Description
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
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
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
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description