GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

• Content
• Detailed Descriptions
• Mappings
• Examples
• XML
• JSON

Resource Profile: Genomic Bundle Profile

A FHIR bundle resource containing genomic data exchange-scoped FHIR profiles.

Usage:

• Examples for this Resource Profile: Bundle/ct-xG-bundle and Bundle/ct-xT-bundle

Formal Views of Profile Content

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

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from Bundle

Name	Flags	Card.	Type	Description & Constraints
Bundle		0..*	Bundle	Contains a collection of resources
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Bundle	C	0..*	Bundle	Contains a collection of resources bdl-1: total only when a search or history bdl-2: entry.search only when a search bdl-3: entry.request mandatory for batch/transaction/history, otherwise prohibited bdl-4: entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited bdl-7: FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) bdl-9: A document must have an identifier with a system and a value bdl-10: A document must have a date bdl-11: A document must have a Composition as the first resource bdl-12: A message must have a MessageHeader as the first resource
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
type	Σ	1..1	code	document | message | transaction | transaction-response | batch | batch-response | history | searchset | collection Binding: BundleType (required): Indicates the purpose of a bundle - how it is intended to be used. ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Bundle.type	required	BundleType http://hl7.org/fhir/ValueSet/bundle-type|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
bdl-1	error	Bundle	total only when a search or history : total.empty() or (type = 'searchset') or (type = 'history')
bdl-2	error	Bundle	entry.search only when a search : entry.search.empty() or (type = 'searchset')
bdl-3	error	Bundle	entry.request mandatory for batch/transaction/history, otherwise prohibited : entry.all(request.exists() = (%resource.type = 'batch' or %resource.type = 'transaction' or %resource.type = 'history'))
bdl-4	error	Bundle	entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited : entry.all(response.exists() = (%resource.type = 'batch-response' or %resource.type = 'transaction-response' or %resource.type = 'history'))
bdl-7	error	Bundle	FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) : (type = 'history') or entry.where(fullUrl.exists()).select(fullUrl&resource.meta.versionId).isDistinct()
bdl-9	error	Bundle	A document must have an identifier with a system and a value : type = 'document' implies (identifier.system.exists() and identifier.value.exists())
bdl-10	error	Bundle	A document must have a date : type = 'document' implies (timestamp.hasValue())
bdl-11	error	Bundle	A document must have a Composition as the first resource : type = 'document' implies entry.first().resource.is(Composition)
bdl-12	error	Bundle	A message must have a MessageHeader as the first resource : type = 'message' implies entry.first().resource.is(MessageHeader)
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())

Name	Flags	Card.	Type	Description & Constraints
Bundle	C	0..*	Bundle	Contains a collection of resources bdl-1: total only when a search or history bdl-2: entry.search only when a search bdl-3: entry.request mandatory for batch/transaction/history, otherwise prohibited bdl-4: entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited bdl-7: FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) bdl-9: A document must have an identifier with a system and a value bdl-10: A document must have a date bdl-11: A document must have a Composition as the first resource bdl-12: A message must have a MessageHeader as the first resource
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
identifier	Σ	0..1	Identifier	Persistent identifier for the bundle
type	Σ	1..1	code	document | message | transaction | transaction-response | batch | batch-response | history | searchset | collection Binding: BundleType (required): Indicates the purpose of a bundle - how it is intended to be used.
timestamp	Σ	0..1	instant	When the bundle was assembled
total	ΣC	0..1	unsignedInt	If search, the total number of matches
link	Σ	0..*	BackboneElement	Links related to this Bundle
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
relation	Σ	1..1	string	See http://www.iana.org/assignments/link-relations/link-relations.xhtml#link-relations-1
url	Σ	1..1	uri	Reference details for the link
entry	ΣC	0..*	BackboneElement	Entry in the bundle - will have a resource or information bdl-5: must be a resource unless there's a request or response bdl-8: fullUrl cannot be a version specific reference This repeating element order: For bundles of type 'document' and 'message', the first resource is special (must be Composition or MessageHeader respectively). For all bundles, the meaning of the order of entries depends on the bundle type
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
link	Σ	0..*	See link (Bundle)	Links related to this entry
fullUrl	Σ	0..1	uri	URI for resource (Absolute URL server address or URI for UUID/OID)
resource	Σ	0..1	Resource	A resource in the bundle
search	ΣC	0..1	BackboneElement	Search related information
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
mode	Σ	0..1	code	match | include | outcome - why this is in the result set Binding: SearchEntryMode (required): Why an entry is in the result set - whether it's included as a match or because of an _include requirement, or to convey information or warning information about the search process.
score	Σ	0..1	decimal	Search ranking (between 0 and 1)
request	ΣC	0..1	BackboneElement	Additional execution information (transaction/batch/history)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
method	Σ	1..1	code	GET | HEAD | POST | PUT | DELETE | PATCH Binding: HTTPVerb (required): HTTP verbs (in the HTTP command line). See HTTP rfc for details.
url	Σ	1..1	uri	URL for HTTP equivalent of this entry
ifNoneMatch	Σ	0..1	string	For managing cache currency
ifModifiedSince	Σ	0..1	instant	For managing cache currency
ifMatch	Σ	0..1	string	For managing update contention
ifNoneExist	Σ	0..1	string	For conditional creates
response	ΣC	0..1	BackboneElement	Results of execution (transaction/batch/history)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
status	Σ	1..1	string	Status response code (text optional)
location	Σ	0..1	uri	The location (if the operation returns a location)
etag	Σ	0..1	string	The Etag for the resource (if relevant)
lastModified	Σ	0..1	instant	Server's date time modified
outcome	Σ	0..1	Resource	OperationOutcome with hints and warnings (for batch/transaction)
signature	Σ	0..1	Signature	Digital Signature
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Bundle.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Bundle.type	required	BundleType http://hl7.org/fhir/ValueSet/bundle-type|4.0.1 from the FHIR Standard
Bundle.entry.search.mode	required	SearchEntryMode http://hl7.org/fhir/ValueSet/search-entry-mode|4.0.1 from the FHIR Standard
Bundle.entry.request.method	required	HTTPVerb http://hl7.org/fhir/ValueSet/http-verb|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
bdl-1	error	Bundle	total only when a search or history : total.empty() or (type = 'searchset') or (type = 'history')
bdl-2	error	Bundle	entry.search only when a search : entry.search.empty() or (type = 'searchset')
bdl-3	error	Bundle	entry.request mandatory for batch/transaction/history, otherwise prohibited : entry.all(request.exists() = (%resource.type = 'batch' or %resource.type = 'transaction' or %resource.type = 'history'))
bdl-4	error	Bundle	entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited : entry.all(response.exists() = (%resource.type = 'batch-response' or %resource.type = 'transaction-response' or %resource.type = 'history'))
bdl-5	error	Bundle.entry	must be a resource unless there's a request or response : resource.exists() or request.exists() or response.exists()
bdl-7	error	Bundle	FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) : (type = 'history') or entry.where(fullUrl.exists()).select(fullUrl&resource.meta.versionId).isDistinct()
bdl-8	error	Bundle.entry	fullUrl cannot be a version specific reference : fullUrl.contains('/_history/').not()
bdl-9	error	Bundle	A document must have an identifier with a system and a value : type = 'document' implies (identifier.system.exists() and identifier.value.exists())
bdl-10	error	Bundle	A document must have a date : type = 'document' implies (timestamp.hasValue())
bdl-11	error	Bundle	A document must have a Composition as the first resource : type = 'document' implies entry.first().resource.is(Composition)
bdl-12	error	Bundle	A message must have a MessageHeader as the first resource : type = 'message' implies entry.first().resource.is(MessageHeader)
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()

This structure is derived from Bundle

Summary

Differential View

This structure is derived from Bundle

Name	Flags	Card.	Type	Description & Constraints
Bundle		0..*	Bundle	Contains a collection of resources
Documentation for this format

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Bundle	C	0..*	Bundle	Contains a collection of resources bdl-1: total only when a search or history bdl-2: entry.search only when a search bdl-3: entry.request mandatory for batch/transaction/history, otherwise prohibited bdl-4: entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited bdl-7: FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) bdl-9: A document must have an identifier with a system and a value bdl-10: A document must have a date bdl-11: A document must have a Composition as the first resource bdl-12: A message must have a MessageHeader as the first resource
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
type	Σ	1..1	code	document | message | transaction | transaction-response | batch | batch-response | history | searchset | collection Binding: BundleType (required): Indicates the purpose of a bundle - how it is intended to be used. ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Bundle.type	required	BundleType http://hl7.org/fhir/ValueSet/bundle-type|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
bdl-1	error	Bundle	total only when a search or history : total.empty() or (type = 'searchset') or (type = 'history')
bdl-2	error	Bundle	entry.search only when a search : entry.search.empty() or (type = 'searchset')
bdl-3	error	Bundle	entry.request mandatory for batch/transaction/history, otherwise prohibited : entry.all(request.exists() = (%resource.type = 'batch' or %resource.type = 'transaction' or %resource.type = 'history'))
bdl-4	error	Bundle	entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited : entry.all(response.exists() = (%resource.type = 'batch-response' or %resource.type = 'transaction-response' or %resource.type = 'history'))
bdl-7	error	Bundle	FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) : (type = 'history') or entry.where(fullUrl.exists()).select(fullUrl&resource.meta.versionId).isDistinct()
bdl-9	error	Bundle	A document must have an identifier with a system and a value : type = 'document' implies (identifier.system.exists() and identifier.value.exists())
bdl-10	error	Bundle	A document must have a date : type = 'document' implies (timestamp.hasValue())
bdl-11	error	Bundle	A document must have a Composition as the first resource : type = 'document' implies entry.first().resource.is(Composition)
bdl-12	error	Bundle	A message must have a MessageHeader as the first resource : type = 'message' implies entry.first().resource.is(MessageHeader)
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Bundle	C	0..*	Bundle	Contains a collection of resources bdl-1: total only when a search or history bdl-2: entry.search only when a search bdl-3: entry.request mandatory for batch/transaction/history, otherwise prohibited bdl-4: entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited bdl-7: FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) bdl-9: A document must have an identifier with a system and a value bdl-10: A document must have a date bdl-11: A document must have a Composition as the first resource bdl-12: A message must have a MessageHeader as the first resource
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
identifier	Σ	0..1	Identifier	Persistent identifier for the bundle
type	Σ	1..1	code	document | message | transaction | transaction-response | batch | batch-response | history | searchset | collection Binding: BundleType (required): Indicates the purpose of a bundle - how it is intended to be used.
timestamp	Σ	0..1	instant	When the bundle was assembled
total	ΣC	0..1	unsignedInt	If search, the total number of matches
link	Σ	0..*	BackboneElement	Links related to this Bundle
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
relation	Σ	1..1	string	See http://www.iana.org/assignments/link-relations/link-relations.xhtml#link-relations-1
url	Σ	1..1	uri	Reference details for the link
entry	ΣC	0..*	BackboneElement	Entry in the bundle - will have a resource or information bdl-5: must be a resource unless there's a request or response bdl-8: fullUrl cannot be a version specific reference This repeating element order: For bundles of type 'document' and 'message', the first resource is special (must be Composition or MessageHeader respectively). For all bundles, the meaning of the order of entries depends on the bundle type
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
link	Σ	0..*	See link (Bundle)	Links related to this entry
fullUrl	Σ	0..1	uri	URI for resource (Absolute URL server address or URI for UUID/OID)
resource	Σ	0..1	Resource	A resource in the bundle
search	ΣC	0..1	BackboneElement	Search related information
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
mode	Σ	0..1	code	match | include | outcome - why this is in the result set Binding: SearchEntryMode (required): Why an entry is in the result set - whether it's included as a match or because of an _include requirement, or to convey information or warning information about the search process.
score	Σ	0..1	decimal	Search ranking (between 0 and 1)
request	ΣC	0..1	BackboneElement	Additional execution information (transaction/batch/history)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
method	Σ	1..1	code	GET | HEAD | POST | PUT | DELETE | PATCH Binding: HTTPVerb (required): HTTP verbs (in the HTTP command line). See HTTP rfc for details.
url	Σ	1..1	uri	URL for HTTP equivalent of this entry
ifNoneMatch	Σ	0..1	string	For managing cache currency
ifModifiedSince	Σ	0..1	instant	For managing cache currency
ifMatch	Σ	0..1	string	For managing update contention
ifNoneExist	Σ	0..1	string	For conditional creates
response	ΣC	0..1	BackboneElement	Results of execution (transaction/batch/history)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
status	Σ	1..1	string	Status response code (text optional)
location	Σ	0..1	uri	The location (if the operation returns a location)
etag	Σ	0..1	string	The Etag for the resource (if relevant)
lastModified	Σ	0..1	instant	Server's date time modified
outcome	Σ	0..1	Resource	OperationOutcome with hints and warnings (for batch/transaction)
signature	Σ	0..1	Signature	Digital Signature
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Bundle.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Bundle.type	required	BundleType http://hl7.org/fhir/ValueSet/bundle-type|4.0.1 from the FHIR Standard
Bundle.entry.search.mode	required	SearchEntryMode http://hl7.org/fhir/ValueSet/search-entry-mode|4.0.1 from the FHIR Standard
Bundle.entry.request.method	required	HTTPVerb http://hl7.org/fhir/ValueSet/http-verb|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
bdl-1	error	Bundle	total only when a search or history : total.empty() or (type = 'searchset') or (type = 'history')
bdl-2	error	Bundle	entry.search only when a search : entry.search.empty() or (type = 'searchset')
bdl-3	error	Bundle	entry.request mandatory for batch/transaction/history, otherwise prohibited : entry.all(request.exists() = (%resource.type = 'batch' or %resource.type = 'transaction' or %resource.type = 'history'))
bdl-4	error	Bundle	entry.response mandatory for batch-response/transaction-response/history, otherwise prohibited : entry.all(response.exists() = (%resource.type = 'batch-response' or %resource.type = 'transaction-response' or %resource.type = 'history'))
bdl-5	error	Bundle.entry	must be a resource unless there's a request or response : resource.exists() or request.exists() or response.exists()
bdl-7	error	Bundle	FullUrl must be unique in a bundle, or else entries with the same fullUrl must have different meta.versionId (except in history bundles) : (type = 'history') or entry.where(fullUrl.exists()).select(fullUrl&resource.meta.versionId).isDistinct()
bdl-8	error	Bundle.entry	fullUrl cannot be a version specific reference : fullUrl.contains('/_history/').not()
bdl-9	error	Bundle	A document must have an identifier with a system and a value : type = 'document' implies (identifier.system.exists() and identifier.value.exists())
bdl-10	error	Bundle	A document must have a date : type = 'document' implies (timestamp.hasValue())
bdl-11	error	Bundle	A document must have a Composition as the first resource : type = 'document' implies entry.first().resource.is(Composition)
bdl-12	error	Bundle	A message must have a MessageHeader as the first resource : type = 'message' implies entry.first().resource.is(MessageHeader)
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()

This structure is derived from Bundle

Summary

Other representations of profile: CSV, Excel, Schematron