NCPI File Meta Data - NCPI FHIR Implementation Guide v2 v0.1.0

NCPI FHIR Implementation Guide v2
0.1.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: NCPI File Meta Data

Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata				Version: 0.1.0
Draft as of 2025-03-24				Computable Name: NcpiFileMetadata

Representation of file metadata for NCPI

Key Guidelines

The NCPI File Metadata profile is based on the standard resource type, Observation and is intended to represent information about the file metadata associated with a file.

Added Profile Restrictions

In order to ensure that our resources are interoperable across studies, we have employed a number of restrictions that should make consuming Patient resources more consistent.

The NCPI File Metadata profile is essentially a collection of slices built on one another.

Recommended Practices

This IG supports FASTQ, BAM/CRAM, MAF, VCF, and Proteomics file types, all of which use the NCPI File Metadata profile as its Parent. Each file has a set of expectations for pieces of information to include based on the specific needs of each file type.

FHIR Mappings

The following fields from the shared data model are to be mapped to the NCPI File Metadata as shown below:

Logical Model Property	Cardinality	NCPI FHIR Mapping	Usage Guidance	Notes
parent_file	1..1	focus	A Reference to a file to which the metadata is related
assay_strategy	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	e.g., Whole Genome Sequencing
platform_instrument	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	e.g., Illumina HiSeq2000
library_prep	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	e.g., polyA
library_selection	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component
strandedness	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	stranded, unstranded
target_region	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component
is_paired_end	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	True, False
adaptor_trimmed	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	True, False
reference_genome	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	GRCh37, GRCh38
workflow_type	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	e.g., alignment, somatic
workflow_tool	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Observation.component	e.g., BAM-MEM, GATK-Haplotype Caller
specimen_collection	BAM/CRAM, FASTQ, MAF, Proteomics, VCF	Extension Reference(Any)	e.g., Reference(Participant_ID)

Usage:

Derived from this Resource Profile: BAM or CRAM file profile, NCPI FASTQ File, Gene fusion or gene expression file profile, MAF (Somatic Mutation) file profile... Show 2 more

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	Observation	Measurements and simple assertions dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
status	?!Σ	1..1	code	registered \| preliminary \| final \| amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children
code	Σ	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children
focus	Σ	1..1	Reference(Resource)	What the observation is about, when it is not about the subject of record ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Observation.status	required	ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status\|4.3.0` from the FHIR Standard
Observation.code	example	LOINCCodes (a valid code from LOINC) `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	ALL elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	ALL extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from Observation

Name	Card.	Type	Description & Constraints
Observation	0..*	Observation	Measurements and simple assertions
focus	1..1	Reference(Resource)	What the observation is about, when it is not about the subject of record
Documentation for this format

Description & Constraints

Observation

C

0..*

Observation

Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present

id

Σ

0..1

id

Logical id of this artifact

Terminology Bindings

Path Conformance ValueSet URI

Observation.language

preferred

CommonLanguages

http://hl7.org/fhir/ValueSet/languages

from the FHIR Standard

Additional Bindings

Purpose

AllLanguages

Max Binding

Observation.status

required

ObservationStatus

http://hl7.org/fhir/ValueSet/observation-status|4.3.0

from the FHIR Standard

Observation.category

preferred

ObservationCategoryCodes

http://hl7.org/fhir/ValueSet/observation-category

from the FHIR Standard

Observation.code

example

LOINCCodes (a valid code from LOINC)

http://hl7.org/fhir/ValueSet/observation-codes

from the FHIR Standard

Observation.dataAbsentReason

extensible

DataAbsentReason

http://hl7.org/fhir/ValueSet/data-absent-reason

from the FHIR Standard

Observation.interpretation

extensible

ObservationInterpretationCodes

http://hl7.org/fhir/ValueSet/observation-interpretation

from the FHIR Standard

Observation.bodySite

example

SNOMEDCTBodyStructures

http://hl7.org/fhir/ValueSet/body-site

from the FHIR Standard

Observation.method

example

ObservationMethods

http://hl7.org/fhir/ValueSet/observation-methods

from the FHIR Standard

Observation.referenceRange.type

preferred

ObservationReferenceRangeMeaningCodes

http://hl7.org/fhir/ValueSet/referencerange-meaning

from the FHIR Standard

Observation.referenceRange.appliesTo

example

ObservationReferenceRangeAppliesToCodes

http://hl7.org/fhir/ValueSet/referencerange-appliesto

from the FHIR Standard

Observation.component.code

example

LOINCCodes (a valid code from LOINC)

http://hl7.org/fhir/ValueSet/observation-codes

from the FHIR Standard

Observation.component.dataAbsentReason

extensible

DataAbsentReason

http://hl7.org/fhir/ValueSet/data-absent-reason

from the FHIR Standard

Observation.component.interpretation

extensible

ObservationInterpretationCodes

http://hl7.org/fhir/ValueSet/observation-interpretation

from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management : text.`div`.exists()
dom-r4b	warning	Observation.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
ele-1	error	ALL elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	ALL extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text : low.exists() or high.exists() or text.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	Observation	Measurements and simple assertions dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
status	?!Σ	1..1	code	registered \| preliminary \| final \| amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children
code	Σ	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children
focus	Σ	1..1	Reference(Resource)	What the observation is about, when it is not about the subject of record ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Observation.status	required	ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status\|4.3.0` from the FHIR Standard
Observation.code	example	LOINCCodes (a valid code from LOINC) `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	ALL elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	ALL extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from Observation

Name	Card.	Type	Description & Constraints
Observation	0..*	Observation	Measurements and simple assertions
focus	1..1	Reference(Resource)	What the observation is about, when it is not about the subject of record
Documentation for this format

Snapshot View

Description & Constraints

Observation

C

0..*

Observation

Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present

id

Σ

0..1

id

Logical id of this artifact

Terminology Bindings

Path Conformance ValueSet URI

Observation.language

preferred

CommonLanguages

http://hl7.org/fhir/ValueSet/languages

from the FHIR Standard

Additional Bindings

Purpose

AllLanguages

Max Binding

Observation.status

required

ObservationStatus

http://hl7.org/fhir/ValueSet/observation-status|4.3.0

from the FHIR Standard

Observation.category

preferred

ObservationCategoryCodes

http://hl7.org/fhir/ValueSet/observation-category

from the FHIR Standard

Observation.code

example

LOINCCodes (a valid code from LOINC)

http://hl7.org/fhir/ValueSet/observation-codes

from the FHIR Standard

Observation.dataAbsentReason

extensible

DataAbsentReason

http://hl7.org/fhir/ValueSet/data-absent-reason

from the FHIR Standard

Observation.interpretation

extensible

ObservationInterpretationCodes

http://hl7.org/fhir/ValueSet/observation-interpretation

from the FHIR Standard

Observation.bodySite

example

SNOMEDCTBodyStructures

http://hl7.org/fhir/ValueSet/body-site

from the FHIR Standard

Observation.method

example

ObservationMethods

http://hl7.org/fhir/ValueSet/observation-methods

from the FHIR Standard

Observation.referenceRange.type

preferred

ObservationReferenceRangeMeaningCodes

http://hl7.org/fhir/ValueSet/referencerange-meaning

from the FHIR Standard

Observation.referenceRange.appliesTo

example

ObservationReferenceRangeAppliesToCodes

http://hl7.org/fhir/ValueSet/referencerange-appliesto

from the FHIR Standard

Observation.component.code

example

LOINCCodes (a valid code from LOINC)

http://hl7.org/fhir/ValueSet/observation-codes

from the FHIR Standard

Observation.component.dataAbsentReason

extensible

DataAbsentReason

http://hl7.org/fhir/ValueSet/data-absent-reason

from the FHIR Standard

Observation.component.interpretation

extensible

ObservationInterpretationCodes

http://hl7.org/fhir/ValueSet/observation-interpretation

from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management : text.`div`.exists()
dom-r4b	warning	Observation.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
ele-1	error	ALL elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	ALL extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text : low.exists() or high.exists() or text.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from Observation

Summary

Mandatory: 1 element

Other representations of profile: CSV, Excel, Schematron

IG © 2023+ NCPI FHIR Working Group. Package ncpi-fhir-implementation-guide-v2#0.1.0 based on FHIR 4.3.0. Generated 2025-03-24
Links: Table of Contents | QA Report