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KF/Include FHIR Input Model

DBT Output Schema for FHIR Ingest

URI: https://carrollaboratory.github.io/kfi-fhir-input

Name: kfi-fhir-input

Classes

Class Description
AccessPolicy Limitations and/or requirements that define how a user may gain access to a p...
Any This is a placeholder for the experimental linkml:any behavior for unions
FamilyRelationship A relationship between individuals in a pedigree or family
FileLocation Details relating to the links where documents are found
FileMetaData Representation of file metadata for NCPI
HasExternalId Has an external ID
        Aliquot A Portion of a sample extracted from a participant
        Family Group of Participants that are related
        Institution Institution related to study or research personnel
        NCPIFile Information about a file related to a research participant
        Participant Research oriented patient
        Practitioner For our purposes, this will be an investigator
        Record One row / entity within the database
                AgeAt These represent a flexible age value that could represent one of the followin...
                AssociatedParty Sponsors, collaborators, and other parties affiliated with a research study
                RelativeDateTime In FHIR, we can express events using relative date/times from the participant...
        ResearchStudy The NCPI Research Study FHIR resource represents an individual research effor...
        ResearchStudyCollection Collections of research data including, but not limited, to Consortia, Progra...
        Sample Sample encompasses biospecimen collection, sample information, and aliquot in...
ParticipantAssertion Assertion about a particular Participant
Period Time period associated with some FHIR resource
Person Relate one or more participants to a single person entity
PractitionerRole PractitionerRole covers the recording of the location and types of services t...
StudyMembership Grouping subject participation within a research study is helpful to provide ...

Slots

Slot Description
access_policy_code A classification of the type of consents found in a consent statement
access_policy_id Access Policy Global ID
adaptor_trimmed True, False
age Age either numeric value or range
age_at_assertion The date or age at which this condition is being asserted
age_at_collection The age at which this biospecimen was collected
age_at_event The date or age at which the event relating to this assertion occured
age_at_last_vital Age or date of last vital status
age_at_onset The age of onset for this condition
age_at_resolution The age at which this condition was resolved, abated, or cured
age_code Age expressed as an enumerated value representing an age category
aliquot_id Aliquot Global ID
as_date Event Date (rather than age)
assay_strategy e
assertion_code The structured term defining the meaning of the assertion
assertion_source Where or how was this this assertion about the Participant recorded? This can...
assertion_text Detailed description / free text about this assertion
assertion_type Describe the type of assertion being made
associated_party_institution_id Associated Party (is Institution)
associated_party_practitioner_id Associated Party (is Practitioner)
associated_party_practitioner_role_id Associated Party (is Practitioner Role)
availability_status Can this Sample be requested for further analysis?
birthsex Sex assigned at birth (or pre-natal observed sex)
body_laterality Laterality information for the condition site
body_location Any location qualifiers
body_site Location information for the observation, including site, laterality, and oth...
cancer_stage Cancer staging information
classifier Research Study Party Organization Type (what type of institution is party)
collection_method The approach used to collect the biospecimen ([LOINC](https://loinc
collection_site The location of the specimen collection
collection_status The current state of the collection
collection_title The collection's title
concentration What is the concentration of the analyte in the Aliquot?
concentration_units Units for the aliquot concentration (ucum)
consanguinity Is there known or suspected consanguinity in this study family?
consent_scope Which of the four areas this resource covers (extensible)
content_version Version of the file content
data_access_type Type of access restrictions on file downloads ( open
deceased_rel Implementers can provide relativeDateTime if information is available
description More details associated with the given resource
disease_limitation Disease Use Limitations
dob Date of Birth of the participant
dob_method Specifies method used to alter DOB for research sharing
email An email address to reach the entity
end End attribute for a FHIR period data type
entity_asserter Who recorded this assertion about the Participant? This can support understan...
ethnicity Reported ethnicity as defined by the 1997 OMB directives
external_id Other identifiers for this entity, eg, from the submitting study or in system...
family_focus What is this study family investigating? EG, a specific condition
family_global_id Family Global ID
family_id External ID common to all family members
family_relationship_id Family Relationship Global ID
family_type Describes the 'type' of study family, eg, trio
file_format The file format used ([EDAM](http://edamontology
file_global_id File Global ID
file_hash Value of hashing the file
file_hash_type Algorithm used to calculate the hash (and size, where applicable)
file_location_id Location details (this is not a global ID)
file_meta_data_id Representation of file metadata for NCPI
file_name The file's name (no path)
file_size The size of the file, e
file_size_unit Units associated with the file_size value (ucum)
file_type The type of data contained in this file
id Unique Identifier for a table entry
institution_id The institution this record is associated with
is_deceased Is the participant known to be Deceased, T, or Alive, F
is_paired_end True, False
knowledge_source The source for the reltionship term
label Alias such as acronym and alternate names
laterality Laterality information for the site
library_prep e
library_selection
location_uri The URI at which this data can be accessed
meta_data_type Clarify which type of meta data this file has recorded
name Name of the entity
offset The point after the target being described
offset_end The end of a relative date/time range
offset_type What is the datatype associated with the offset (days, years, etc)
other_condition_modifiers Any additional modifiers for this condition, such as severity
parent_sample_id Sample Global ID associated with the parent sample
parent_study_id ID For Parent Study if this is a substudy
participant_assertion_id Participant Assertion Global ID
participant_id The Global ID for the Participant
party Individual or organization associated with study
patient_id The child from the parent-child relationship
patient_knowledge_source The source of the knowledge represented by this Patient resource
period_id Reference to a time period which defines a Start and End datatime period
person_id Person Global ID (group)
platform_instrument e
population opulation, Race, and/or Ethnicity information
practitioner_id The Global ID for the PractitionerRole that links a Practitioner to their Ins...
practitioner_role_id Global ID for this record
practitioner_title The title of the Investigator, eg, "Assistant Professor"
processing Processing that was applied to the Parent Sample or from the Biospecimen Coll...
quantity The total quantity of the specimen
quantity_units Units associated with the quantity (ucum)
race Reported race as defined by the 1997 OMB directives
reference_genome GRCh37, GRCh38
relationship The role the relative (parent) fills with respect to the patient (child) for ...
relative_id The parent from the parent-child relationship
research_study_collection_id Global ID for this record
research_study_collection_member_id ID associated with a member of the collection (Research Study, Dataset, etc)
research_study_collection_type The type of collection being described
research_study_id The Global ID for the Research Study
role Research Study Party Role
sample_id Sample Global ID
sample_type The type of material of which this Sample is comprised
samples e
spatial_qualifier Any spatial/location qualifiers
start Start attribute for a FHIR period data type
status Indicates the state of the consent
storage_method How is the Sample stored, eg, Frozen or with additives (e
strandedness stranded, unstranded
study_acknowledgement Any attribution or acknowledgements relevant to the study
study_condition The primary focus(es) of the study
study_design Study Design and Study Type ([example ValueSet can be found here](https://hl7
study_focus The primary, non-disease focus(es) of the study
study_membership_id Study Membership Global ID (group)
study_personnel Every study must have at least one Primary Contact defined
study_status The current state of the study
study_title Research Study's formal title
target_region Target region
value_code Value as code
value_number Value as numer
value_string Value as string
value_type Age Value Type
value_units The structured term defining the units of the value (ucum)
volume What is the volume of the Aliquot?
volume_units Units associated with the volume (ucum)
website URL describing the entity this represents
workflow_tool e
workflow_type e

Enumerations

Enumeration Description
EnumAccessPolicyCode Type of research use case allowed
EnumAgeValueType Describes where to look for the data (as value, code, range, etc)
EnumAssertionType Provides options to describe the expressed semantics of a condition
EnumBirthSex Codes for assigning sex at birth as specified by the Office of the National C...
EnumCollectionStatus The current state of the collection
EnumConsanguinity List of codes indicates the level of known consanguinity (blood relation) wit...
EnumConsentScope The four anticipated uses for the Consent Resource
EnumConsentStateCodes Indicates the state of the consent
EnumDataAccessType Enumerated list of access type codes such as 'Open Access', 'Registered Acces...
EnumDobMethod Enumerations for how DOB was constructed
EnumEntityAsserter Who recorded this assertion about the Participant? This can support understan...
EnumEthnicity OMB Codes describing Hispanic or Latino ethnicity
EnumFamilyRelationship What is the relative's relationship to the patient
EnumFamilyType Describes the 'type' of study family, eg, trio
EnumFileMetaDataType Identify the type of profile to use
EnumOffsetType Offset Type
EnumPatientKnowledgeSource The source of the knowledge represented in a Patient resource
EnumPopulation Code describing the population (CDC)
EnumRace OMB Codes describing race
EnumRelationshipKnowledgeSource Indicate if the relationship is real or inferred
EnumResearchCollectionType Research Study Collection Type
EnumResearchStudyPartyOrganizationType Research Study Party Organization Type
EnumResearchStudyPartyRole This is a ResearchStudy's party role
EnumSpecimenAvailability Can this sample be requested for further analysis
EnumStudyStatus Codes indicating the study's current 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