Molecular Sequence

$10 / year

Molecular Sequence resource will be used to hold clinically relevant sequence data in a manner that is both efficient and versatile integrating new and as yet undefined types of genomic and other -omics data that will soon be commonly entered into health records for clinical use. Molecular Sequence will be leveraged by other Fast Healthcare Interoperability Resources (FHIR) resources, including Observation. This is consistent with how all FHIR resources are designed and used.

Complexity

The September 2014 Informative Ballot “Health Level Seven International (HL7) Clinical Genomics, Domain Analysis Model: Clinical Sequencing Release 1” provided guiding use cases, which initially informed development of the initial Standard Genetics profile that is found in Fast Healthcare Interoperability Resources (FHIR) Draft Standard for Trial Use 2 (DSTU2). The same use cases also led to a second Project to develop a MolecularSequence resource (“Develop FHIR sequence resource for Clinical Genomics”). A preliminary effort to address these issues has been explored and published in context of the Substitutable Medical Applications and Reusable Technologies (SMART) Platforms Project and described in an article (“SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps”).

Molecular Sequence is designed to hold genetic sequences in blocks relevant to actionable clinical decision-making. Extensions to Molecular Sequence address complex cases and can associate it with repositories for retrieving a patient’s full sequence data, such as those defined by Global Alliance for Genomics and Health (GA4GH). Other changes include a suite of genetics profiles for other FHIR resources. In addition, the Observation-genetics profile adds new references so that an Observation can report genetics test results to be integrated into the EHR. There are also new genetics-extension profiles for Diagnostic Report, Service Request and Family Member History, respectively, to extend them to report genetics results. All these FHIR genetics profiles the suffix “-genetics” (e.g. “Diagnostic Report-genetics profile”) are given. New profiles on top of DiagnosticReport have been created for reporting HLA genotyping results.

With these resource and profiles, FHIR can support a large set of clinical use cases (see Section 9, 10 and 11) and is thus positioned to address all emergent -omics use cases, including Next-Generation Sequencing (NGS). These tools are simple to implement, will optimize payload sizes, and help developers avoid redundant retrieval of data.

Date Created

2018-09-20

Last Modified

2019-11-01

Version

4.0.1

Update Frequency

Annual

Temporal Coverage

N/A

Spatial Coverage

United States

Source

John Snow Labs; Health Level Seven International;

Source License URL

Source License Requirements

N/A

Source Citation

N/A

Keywords

FHIR, HL7, Medical Terminology, Processes Data, Processes Information, Processes Documentation, Health Information Exchange, Electronic Health Records, FHIR Smart, Smart on FHIR

Other Titles

FHIR Molecular Sequence Resource, Electronic Health Records Exchange Through FHIR

NameDescriptionTypeConstraints
Concept_NameName of the concept in the FHIR structure.stringrequired : 1
Computer_Ready_NameA Computer-ready name (e.g. a token) that identifies the structure - suitable for code generation. Note that this name (and other names relevant for code generation, including element & slice names, codes etc) may collide with reserved words in the relevant target language, and code generators will need to handle this.string-
TypeThe type the structure describes.string-
Dollar_RefThe "$ref" string value contains a Uniform Resource Identifier (URI) which identifies the location of the JSON value being referenced.string-
DescriptionA free text natural language description of the structure and its use.string-
ItemsThe value of the keyword should be an object or an array of objects. If the keyword value is an object, then for the data array to be valid each item of the array should be valid according to the schema in this value.string-
EnumThe enum is used to restrict a value to a fixed set of values. It must be an array with at least one element, where each element is unique.string-
RequiredThe value of the keyword should be an array of unique strings. The data object to be valid should contain all properties with names equal to the elements in the keyword value.string-
ConstThe value of this keyword can be anything. The data is valid if it is deeply equal to the value of the keyword.string-
Concept NameComputer Ready NameTypeDollar RefDescriptionItemsEnumRequiredConst
MolecularSequenceresourceTypeThis is a MolecularSequence resourceMolecularSequence
MolecularSequenceid#/definitions/idThe logical id of the resource as used in the URL for the resource. Once assigned this value never changes.
MolecularSequencemeta#/definitions/MetaThe metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
MolecularSequenceimplicitRules#/definitions/uriA reference to a set of rules that were followed when the resource was constructed and which must be understood when processing the content. Often this is a reference to an implementation guide that defines the special rules along with other profiles etc.
MolecularSequence_implicitRules#/definitions/ElementExtensions for implicitRules
MolecularSequencelanguage#/definitions/codeThe base language in which the resource is written.
MolecularSequence_language#/definitions/ElementExtensions for language
MolecularSequencetext#/definitions/NarrativeA human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
MolecularSequencecontainedarrayThese resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently and nor can they have their own independent transaction scope.{'$ref': '#/definitions/ResourceList'}
MolecularSequenceextensionarrayMay be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension there is a set of requirements that SHALL be met as part of the definition of the extension.{'$ref': '#/definitions/Extension'}
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