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INCLUDE DCC Access Model

LinkML Schema for the internal INCLUDE DCC Access Model

URI: https://includedcc.org/include-access-model

Name: include-access-model

Classes

Class Description
Concept A standardized concept with display information
Dataset Set of files grouped together for release
FileHash Type and value of a file content hash
Record One row / entity within the database
        ActivityDefinition A definition of an activity in this study, eg, a biospecimen collection, inte...
        Aliquot A specific tube or amount of a biospecimen associated with a Sample
        BiospecimenCollection A biospecimen collection event which yields one or more Samples
        Demographics Basic participant demographics summary
        DOI A DOI is a permanent reference with metadata about a digital object
        Encounter An event at which data was collected about a participant, an intervention was...
        EncounterDefinition A definition of an encounter type in this study, ie, an event at which data w...
        File File
        Investigator An individual who made contributions to the collection, analysis, or sharing ...
        Publication Information about a specific publication
        Sample A functionally equivalent specimen taken from a participant or processed from...
        Study Study Metadata
        StudyMetadata Additional features about studies that may not apply to all studies
        Subject This entity is the subject about which data or references are recorded
        SubjectAssertion Assertion about a particular Subject
        VirtualBiorepository An organization that can provide access to specimen for further analysis

Slots

Slot Description
acknowledgments Funding statement and acknowledgments for this study
activity_definition_id Unique identifier for this Activity Definition
actual_number_of_participants Total participants included at this time
age_at_assertion The age in days of the Subject when the assertion was made
age_at_collection The age at which this biospecimen was collected in decimal years
age_at_event The age in days of the Subject at the time point which the assertion describe...
age_at_first_engagement Age in days of Participant at first recorded study event (enrollment, visit, ...
age_at_last_vital_status Age in days when participant's vital status was last recorded
age_at_resolution The age in days of the Subject when the asserted state was resolved
aliquot_id Unique identifier for an Aliquot
assertion_id INCLUDE Global ID for the Assertion
assertion_provenance The original source of this assertion
availablity_status Can this Sample be requested for further analysis?
bibliographic_reference Text use to reference this Record
biospecimen_collection_id Unique identifier for this Biospecimen Collection
citation_statement Statement that secondary data users should use to acknowledge use of this stu...
clinical_data_source_type Source(s) of data collected from study participants
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
concept The structured term defining the meaning of the assertion
concept_curie The standardized curie for the term
concept_source The source text yielding the standardized concept
contact The individual to contact with questions about this record
data_category General category of data in this Record (e
data_collection_end The date that data collection started
data_collection_start The date that data collection started
data_type The type of data within this file
dataset_id Unique identifier for a Dataset
description Description for this entity
display The friendly display string of the coded term
do_id Digital Object Identifier (DOI) for this Record
down_syndrome_status Down Syndrome status of participant
drs_uri DRS location to access the data
email An email address to reach the entity
encounter_definition_id Unique identifier for this Encounter Definition
encounter_id Unique identifier for this Encounter
ethnicity Ethnicity of Participant
expected_number_of_participants Total expected number of participants to be recruited
external_id Other identifiers for this entity, eg, from the submitting study or in system...
file_id Unique identifier for this File
filename The name of the file
format The format of the file
funding_source The funding source(s) of the study
hash File hash information
hash_type The type of file hash, eg, md5
hash_value The value of the file hash
institution Name of the institution this record is associated with
investigator_title The title of the Investigator, eg, "Assistant Professor"
laterality Laterality that further refine the specific location of biospecimen collectio...
method The approach used to collect the biospecimen
name Name of the entity
organism_type Organism Type
parent_sample_id Sample from which this sample is derived
parent_study The parent study for this study, if it is a nested study
participant_lifespan_stage Focus age group(s) of the study population
principal_investigator The Principal Investigator(s) responsible for the study
processing Processing that was applied to the Parent Sample or from the Biospecimen Coll...
program Funding source(s) for the study
publication Publications associated with this Record
quantity_number The total quantity of the specimen
quantity_unit The structured term defining the units of the quantity
race Race of Participant
release_url URL for controlled or open access to the data
research_domain Main research domain(s) of the study, other than Down syndrome
sample_id The unique identifier for this Sample
sample_type Type of material of which this Sample is comprised
selection_criteria Brief description of inclusion and/or exclusion criteria for the study
sex Sex of Participant
site The location of the specimen collection
size Size of the file, in Bytes
spatial_qualifier Qualifier that further refine the specific location of biospecimen collection
staging_url URL for internal access to the data
storage_method Sample storage method, eg, Frozen or with additives
study_code Unique identifier for the study (generally a short acronym)
study_description Brief description of the study (2-4 sentences)
study_design Overall design of study, including whether it is longitudinal and whether fam...
study_id INCLUDE Global ID for the study
study_short_name Short name for the study
study_title Full Study Title
subject_id INCLUDE Global ID for the Subject
subject_type Type of entity this record represents
value_concept The structured term defining the value of the assertion
value_number The numeric value of the assertion
value_source The source text yielding the value
value_unit The structured term defining the units of the value
value_unit_source The source text yielding the value's units
vbr Information about the study's Virtual Biorepository, if participating
vbr_readme Instructions for contacting or requesting samples from Virtual Biorepository,...
vital_status Whether participant is alive or dead
website Website for the Record

Enumerations

Enumeration Description
EnumAssertionProvenance Possible data sources for assertions
EnumAvailabilityStatus Is the biospecimen available for use?
EnumClinicalDataSourceType Approaches to ascertain clinical information about a participant
EnumDataCategory Categories of data which may be collected about participants
EnumDownSyndromeStatus Down syndrome / chromosome 21 status
EnumEDAMDataTypes Data types from the EDAM ontology
EnumEDAMFormats Data formats from the EDAM ontology
EnumEthnicity Participant ethnicity, specific to Hispanic or Latino
EnumFileHashType Types of file hashes supported
EnumLaterality Laterality information for the site
EnumNull Base enumeration providing null options
EnumParticipantLifespanStage Stages of life during which participants may be recruited
EnumProgram Funding programs relevant to inform operations
EnumRace Participant Race
EnumResearchDomain Domains of Research used to find studies
EnumSampleCollectionMethod The approach used to collect the biospecimen
EnumSex Subject Sex
EnumSite The location of the specimen collection
EnumSpatialQualifiers Any spatial/location qualifiers
EnumStudyDesign Approaches for collecting data, investigating interventions, and/or analyzing...
EnumSubjectType Types of Subject entities
EnumVitalStatus Descriptions of a Subject's vital status

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