DiagnosticReportMicrobiology

Introduction

The DiagnosticReportMicrobiology profile is used for retrieving data about a complete microbiology report for a patient end to end starting from request. This profile is based on the FHIR resource DiagnosticReport.This profile is derived from a core profile created for DiagnosticReport named DiagnosticReportCore. The data available from COSMIC to this profile is only starting from R8.3.03 COSMIC release, information created before this release cannot be taken from this API.

Intended Use

This profile is created as the main profile for the exposing information related to Microbiology report.This profile is based on the core DiagnosticReport profile that is defined for exposing all types of report based resources.

The intended use for reading data with this API is in first hand that the API is applied for direct access and should not be used to transfer data between caregivers. If it should be used for "data copying" between care providers, patient consent must be handled outside the API.

Specific Rules and Limitations

Type	Description
Rule	External user should only be the patient that has the Microbiology report. E.g. A healthcare professional is not the intended user of the API.
Rule	The consumer of the API is responsible for making sure data retrieved is filtered in compliance with laws and regulations prior to presenting it to any end-users.
Rule	For reading diagnostic reports, the external system needs to be able to evaluate PDL. This means whether the information can be displayed for a healthcare professional with a specific assignment. PDL data needed (HSA care unit and HSA care provider) is retrieved by including the organization referenced from DiagnosticReport.performer.OrganizationSEVendorLite.

Profile Overview

DiagnosticReportMicrobiology

DiagnosticReportMicrobiology (DiagnosticReport)	I		DiagnosticReportCore	There are no (further) constraints on this element Element id DiagnosticReport Short description A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports Alternate names Report, Test, Result, Results, Labs, Laboratory Definition The findings and interpretation of diagnostic tests performed on patients, groups of patients, devices, and locations, and/or specimens derived from these. The report includes clinical context such as requesting and provider information, and some mix of atomic results, images, textual and coded interpretations, and formatted representation of diagnostic reports. Comments This is intended to capture a single report and is not suitable for use in displaying summary information that covers multiple reports. For example, this resource has not been designed for laboratory cumulative reporting formats nor detailed structured reports for sequencing. Data type DiagnosticReportCore Constraints dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources `contained.contained.empty()` dom-4: 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-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 `contained.where((('#'+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(canonical) = '#').exists()).not()).trace('unmatched', id).empty()` dom-6: A resource should have narrative for robust management text.`div`.exists() dom-5: If a resource is contained in another resource, it SHALL NOT have a security label `contained.meta.security.empty()` Mappings rim: Entity. Role, or Act workflow: Event v2: ORU -> OBR rim: Observation[classCode=OBS, moodCode=EVN]
id	Σ	1..1	string	There are no (further) constraints on this element Element id DiagnosticReport.id Short description Logical id of this artifact Definition The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. Comments The only time that a resource does not have an id is when it is being submitted to the server using a create operation. Data type string
meta	Σ	0..1	Meta	There are no (further) constraints on this element Element id DiagnosticReport.meta Short description Metadata about the resource Definition The 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. Data type Meta Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
implicitRules	Σ ?!	0..1	uri	There are no (further) constraints on this element Element id DiagnosticReport.implicitRules Short description A set of rules under which this content was created Definition A 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. Comments Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
language		0..1	codeBinding	There are no (further) constraints on this element Element id DiagnosticReport.language Short description Language of the resource content Definition The base language in which the resource is written. Comments Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). Data type code Binding A human language. CommonLanguages (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
text		0..1	Narrative	There are no (further) constraints on this element Element id DiagnosticReport.text Short description Text summary of the resource, for human interpretation Alternate names narrative, html, xhtml, display Definition A 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. Comments Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. Data type Narrative Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A rim: Act.text?
contained		0..*	Resource	There are no (further) constraints on this element Element id DiagnosticReport.contained Short description Contained, inline Resources Alternate names inline resources, anonymous resources, contained resources Definition These 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. Comments This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. Data type Resource Mappings rim: Entity. Role, or Act rim: N/A
extension	I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May 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. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	?! I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.modifierExtension Short description Extensions that cannot be ignored Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
identifier	Σ	0..*	Identifier	There are no (further) constraints on this element Element id DiagnosticReport.identifier Short description Business identifier for report Alternate names ReportID, Filler ID, Placer ID Definition Identifiers assigned to this report by the performer or other systems. Requirements Need to know what identifier to use when making queries about this report from the source laboratory, and for linking to the report outside FHIR context. Comments Usually assigned by the Information System of the diagnostic service provider (filler id). Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier workflow: Event.identifier w5: FiveWs.identifier v2: OBR-51/ for globally unique filler ID - OBR-3 , For non-globally unique filler-id the flller/placer number must be combined with the universal service Id - OBR-2(if present)+OBR-3+OBR-4 rim: id
basedOn	I	1..1	Reference(ServiceRequest)	Element id DiagnosticReport.basedOn Short description What was requested Alternate names Request Definition Details concerning a service requested.(the microbiology request information referenced here) Requirements This allows tracing of authorization for the report and tracking whether proposals/recommendations were acted upon. Comments Note: Usually there is one test request for each result, however in some circumstances multiple test requests may be represented using a single test result resource. Note that there are also cases where one request leads to multiple reports. Data type Reference(ServiceRequest) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.basedOn v2: ORC? OBR-2/3? rim: outboundRelationship[typeCode=FLFS].target
status	Σ ?!	1..1	codeBinding	There are no (further) constraints on this element Element id DiagnosticReport.status Short description registered \| partial \| preliminary \| final + Definition The status of the diagnostic report. Requirements Diagnostic services routinely issue provisional/incomplete reports, and sometimes withdraw previously released reports. Comments Note that FHIR strings SHALL NOT exceed 1MB in size Data type code Binding The status of the diagnostic report. DiagnosticReportStatus (required) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.status w5: FiveWs.status v2: OBR-25 (not 1:1 mapping) rim: statusCode Note: final and amended are distinguished by whether observation is the subject of a ControlAct event of type "revise"
category	Σ	0..*	CodeableConcept	There are no (further) constraints on this element Element id DiagnosticReport.category Short description Service category Alternate names Department, Sub-department, Service, Discipline Definition A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes. Comments Multiple categories are allowed using various categorization schemes. The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code. Data type CodeableConcept Binding Codes for diagnostic service sections. DiagnosticServiceSectionCodes (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD w5: FiveWs.class v2: OBR-24 rim: inboundRelationship[typeCode=COMP].source[classCode=LIST, moodCode=EVN, code < LabService].code
id		0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.category.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.category.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. 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. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a
coding	Σ	0..*	Coding	There are no (further) constraints on this element Element id DiagnosticReport.category.coding Short description Code defined by a terminology system Definition A reference to a code defined by a terminology system. Requirements Allows for alternative encodings within a code system, and translations to other code systems. Comments Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true. Data type Coding Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.1-8, CE.10-22 rim: union(., ./translation) orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
id		0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. 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. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a
system	Σ	0..1	uri	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.system Short description Identity of the terminology system Definition The identification of the code system that defines the meaning of the symbol in the code. Requirements Need to be unambiguous about the source of the definition of the symbol. Comments The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.3 rim:* ./codeSystem orim: fhir:Coding.system rdfs:subPropertyOf dt:CDCoding.codeSystem
version	Σ	0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.version Short description Version of the system - if relevant Definition The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged. Comments Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.7 rim:* ./codeSystemVersion orim: fhir:Coding.version rdfs:subPropertyOf dt:CDCoding.codeSystemVersion
code	Σ	0..1	codeFixed Value	Element id DiagnosticReport.category.coding.code Short description Symbol in syntax defined by the system Definition A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination). Requirements Need to refer to a particular code in the system. Data type code Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Fixed value MB Mappings v2: CE.1 rim:* ./code orim: fhir:Coding.code rdfs:subPropertyOf dt:CDCoding.code
display	Σ	0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.display Short description Representation defined by the system Definition A representation of the meaning of the code in the system, following the rules of the system. Requirements Need to be able to carry a human-readable meaning of the code for readers that do not know the system. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.2 - but note this is not well followed rim:* CV.displayName orim: fhir:Coding.display rdfs:subPropertyOf dt:CDCoding.displayName
userSelected	Σ	0..1	boolean	There are no (further) constraints on this element Element id DiagnosticReport.category.coding.userSelected Short description If this coding was chosen directly by the user Definition Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays). Requirements This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing. Comments Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely. Data type boolean Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: Sometimes implied by being first rim: CD.codingRationale orim: fhir:Coding.userSelected fhir:mapsTo dt:CDCoding.codingRationale. fhir:Coding.userSelected fhir:hasMap fhir:Coding.userSelected.map. fhir:Coding.userSelected.map a fhir:Map; fhir:target dt:CDCoding.codingRationale. fhir:Coding.userSelected\#true a [ fhir:source "true"; fhir:target dt:CDCoding.codingRationale\#O ]
text	Σ	0..1	stringFixed Value	Element id DiagnosticReport.category.text Short description Plain text representation of the concept Definition A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user. Requirements The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source. Comments Very often the text is the same as a displayName of one of the codings. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Fixed value Microbiology Mappings v2: CE.9. But note many systems use CE.2 for this rim: ./originalText[mediaType/code="text/plain"]/data orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
code	Σ	1..1	CodeableConceptBinding	There are no (further) constraints on this element Element id DiagnosticReport.code Short description Name/Code for this diagnostic report Alternate names Type Definition A code or name that describes this diagnostic report. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Codes that describe Diagnostic Reports. LOINCDiagnosticReportCodes (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD workflow: Event.code w5: FiveWs.what[x] v2: OBR-4 (HL7 v2 doesn't provide an easy way to indicate both the ordered test and the performed panel) rim: code
id		0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.code.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.code.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. 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. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a
coding	Σ	0..*	Coding	There are no (further) constraints on this element Element id DiagnosticReport.code.coding Short description Code defined by a terminology system Definition A reference to a code defined by a terminology system. Requirements Allows for alternative encodings within a code system, and translations to other code systems. Comments Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true. Data type Coding Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.1-8, CE.10-22 rim: union(., ./translation) orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
id		0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.code.coding.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id DiagnosticReport.code.coding.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. 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. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a
system	Σ	0..1	uriFixed Value	Element id DiagnosticReport.code.coding.system Short description Identity of the terminology system Definition The identification of the code system that defines the meaning of the symbol in the code. Requirements Need to be unambiguous about the source of the definition of the symbol. Comments The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Fixed value SNOMED CT Mappings v2: CE.3 rim:* ./codeSystem orim: fhir:Coding.system rdfs:subPropertyOf dt:CDCoding.codeSystem
version	Σ	0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.code.coding.version Short description Version of the system - if relevant Definition The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged. Comments Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.7 rim:* ./codeSystemVersion orim: fhir:Coding.version rdfs:subPropertyOf dt:CDCoding.codeSystemVersion
code	Σ	0..1	codeFixed Value	Element id DiagnosticReport.code.coding.code Short description Symbol in syntax defined by the system Definition A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination). Requirements Need to refer to a particular code in the system. Data type code Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Fixed value 4341000179107 Mappings v2: CE.1 rim:* ./code orim: fhir:Coding.code rdfs:subPropertyOf dt:CDCoding.code
display	Σ	0..1	stringFixed Value	Element id DiagnosticReport.code.coding.display Short description Representation defined by the system Definition A representation of the meaning of the code in the system, following the rules of the system. Requirements Need to be able to carry a human-readable meaning of the code for readers that do not know the system. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Fixed value Microbiology report Mappings v2: CE.2 - but note this is not well followed rim:* CV.displayName orim: fhir:Coding.display rdfs:subPropertyOf dt:CDCoding.displayName
userSelected	Σ	0..1	boolean	There are no (further) constraints on this element Element id DiagnosticReport.code.coding.userSelected Short description If this coding was chosen directly by the user Definition Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays). Requirements This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing. Comments Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely. Data type boolean Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: Sometimes implied by being first rim: CD.codingRationale orim: fhir:Coding.userSelected fhir:mapsTo dt:CDCoding.codingRationale. fhir:Coding.userSelected fhir:hasMap fhir:Coding.userSelected.map. fhir:Coding.userSelected.map a fhir:Map; fhir:target dt:CDCoding.codingRationale. fhir:Coding.userSelected\#true a [ fhir:source "true"; fhir:target dt:CDCoding.codingRationale\#O ]
text	Σ	0..1	string	There are no (further) constraints on this element Element id DiagnosticReport.code.text Short description Plain text representation of the concept Definition A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user. Requirements The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source. Comments Very often the text is the same as a displayName of one of the codings. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings v2: CE.9. But note many systems use CE.2 for this rim: ./originalText[mediaType/code="text/plain"]/data orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
subject	Σ I	0..1	Reference(Patient \| Group \| Device \| Location)	There are no (further) constraints on this element Element id DiagnosticReport.subject Short description The subject of the report - usually, but not always, the patient Alternate names Patient Definition The subject of the report. Usually, but not always, this is a patient. However, diagnostic services also perform analyses on specimens collected from a variety of other sources. Requirements SHALL know the subject context. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient \| Group \| Device \| Location) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.subject w5: FiveWs.subject[x] v2: PID-3 (no HL7 v2 mapping for Group or Device) rim: participation[typeCode=SBJ] w5: FiveWs.subject
encounter	Σ I	0..1	Reference(Encounter)	There are no (further) constraints on this element Element id DiagnosticReport.encounter Short description Health care event when test ordered Alternate names Context Definition The healthcare event (e.g. a patient and healthcare provider interaction) which this DiagnosticReport is about. Requirements Links the request to the Encounter context. Comments This will typically be the encounter the event occurred within, but some events may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter (e.g. pre-admission laboratory tests). Data type Reference(Encounter) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.encounter w5: FiveWs.context v2: PV1-19 rim: inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
effective[x]	Σ	0..0		Element id DiagnosticReport.effective[x] Short description Clinically relevant time/time-period for report Alternate names Observation time, Effective Time, Occurrence Definition The time or time-period the observed values are related to. When the subject of the report is a patient, this is usually either the time of the procedure or of specimen collection(s), but very often the source of the date/time is not known, only the date/time itself.(This information do not get from lab systems) Requirements Need to know where in the patient history to file/present this report. Comments If the diagnostic procedure was performed on the patient, this is the time it was performed. If there are specimens, the diagnostically relevant time can be derived from the specimen collection times, but the specimen information is not always available, and the exact relationship between the specimens and the diagnostically relevant time is not always automatic. Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.occurrence[x] w5: FiveWs.done[x] v2: OBR-7 rim: effectiveTime
issued	Σ	0..1	instant	There are no (further) constraints on this element Element id DiagnosticReport.issued Short description DateTime this version was made Alternate names Date published, Date Issued, Date Verified Definition The date and time that this version of the report was made available to providers, typically after the report was reviewed and verified. Requirements Clinicians need to be able to check the date that the report was released. Comments May be different from the update time of the resource itself, because that is the status of the record (potentially a secondary copy), not the actual release time of the report. Data type instant Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a w5: FiveWs.recorded v2: OBR-22 rim: participation[typeCode=VRF or AUT].time
performer	Σ I	0..*	Reference(Practitioner \| Organization \| OrganizationSEVendorLite \| https://fhir.cambio.se/StructureDefinition/OrganizationSEIndustryLite)	Element id DiagnosticReport.performer Short description Responsible Diagnostic Service Alternate names Laboratory, Service, Practitioner, Department, Company, Authorized by, Director Definition The diagnostic service that is responsible for issuing the report. Requirements Need to know whom to contact if there are queries about the results. Also may need to track the source of reports for secondary data analysis. Comments This is not necessarily the source of the atomic data items or the entity that interpreted the results. It is the entity that takes responsibility for the clinical report. Data type Reference(Practitioner \| Organization \| OrganizationSEVendorLite \| https://fhir.cambio.se/StructureDefinition/OrganizationSEIndustryLite) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.performer.actor w5: FiveWs.actor v2: PRT-8 (where this PRT-4-Participation = "PO") rim: .participation[typeCode=PRF]
resultsInterpreter	Σ I	0..*	Reference(Practitioner \| PractitionerRole \| Organization \| CareTeam)	Element id DiagnosticReport.resultsInterpreter Short description Primary result interpreter Alternate names Analyzed by, Reported by Definition The practitioner or organization that is responsible for the report's conclusions and interpretations.(Do not have that information exposed correctly from lab) Requirements Need to know whom to contact if there are queries about the results. Also may need to track the source of reports for secondary data analysis. Comments Might not be the same entity that takes responsibility for the clinical report. Data type Reference(Practitioner \| PractitionerRole \| Organization \| CareTeam) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.performer.actor w5: FiveWs.actor v2: OBR-32, PRT-8 (where this PRT-4-Participation = "PI") rim: .participation[typeCode=PRF]
specimen	I	0..*	Reference(Specimen)	There are no (further) constraints on this element Element id DiagnosticReport.specimen Short description Specimens this report is based on Definition Details about the specimens on which this diagnostic report is based. Requirements Need to be able to report information about the collected specimens on which the report is based. Comments If the specimen is sufficiently specified with a code in the test result name, then this additional data may be redundant. If there are multiple specimens, these may be represented per observation or group. Data type Reference(Specimen) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) v2: SPM rim: participation[typeCode=SBJ]
result	I	0..*	Reference(Observation \| ObservationMicrobiology)	Element id DiagnosticReport.result Short description Observations Alternate names Data, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer Definition Observations that are part of this diagnostic report. Requirements Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful. Comments Observations can contain observations. Data type Reference(Observation \| ObservationMicrobiology) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) v2: OBXs rim: outboundRelationship[typeCode=COMP].target
imagingStudy	I	0..0	Reference(ImagingStudy)	Element id DiagnosticReport.imagingStudy Short description Reference to full details of imaging associated with the diagnostic report Definition One or more links to full details of any imaging performed during the diagnostic investigation. Typically, this is imaging performed by DICOM enabled modalities, but this is not required. A fully enabled PACS viewer can use this information to provide views of the source images.(removed because microbiology do not have imaging information) Comments ImagingStudy and the image element are somewhat overlapping - typically, the list of image references in the image element will also be found in one of the imaging study resources. However, each caters to different types of displays for different types of purposes. Neither, either, or both may be provided. Data type Reference(ImagingStudy) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: outboundRelationship[typeCode=COMP].target[classsCode=DGIMG, moodCode=EVN]
media	Σ	0..0	BackboneElement	There are no (further) constraints on this element Element id DiagnosticReport.media Short description Key images associated with this report Alternate names DICOM, Slides, Scans Definition A list of key images associated with this report. The images are generally created during the diagnostic process, and may be directly of the patient, or of treated specimens (i.e. slides of interest). Requirements Many diagnostic services include images in the report as part of their service. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: OBX? rim: outboundRelationship[typeCode=COMP].target
conclusion		0..0	string	There are no (further) constraints on this element Element id DiagnosticReport.conclusion Short description Clinical conclusion (interpretation) of test results Alternate names Report Definition Concise and clinically contextualized summary conclusion (interpretation/impression) of the diagnostic report. Requirements Need to be able to provide a conclusion that is not lost among the basic result data. Comments Note that FHIR strings SHALL NOT exceed 1MB in size Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: OBX rim: inboundRelationship[typeCode="SPRT"].source[classCode=OBS, moodCode=EVN, code=LOINC:48767-8].value (type=ST)
conclusionCode		0..0	CodeableConcept	Element id DiagnosticReport.conclusionCode Short description Codes for the clinical conclusion of test results Definition One or more codes that represent the summary conclusion (interpretation/impression) of the diagnostic report.(we do not have any codes related to conclusion) Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Diagnosis codes provided as adjuncts to the report. SNOMEDCTClinicalFindings (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: OBX rim: inboundRelationship[typeCode=SPRT].source[classCode=OBS, moodCode=EVN, code=LOINC:54531-9].value (type=CD)
presentedForm	I	0..0	Attachment	There are no (further) constraints on this element Element id DiagnosticReport.presentedForm Short description Entire report as issued Definition Rich text representation of the entire result as issued by the diagnostic service. Multiple formats are allowed but they SHALL be semantically equivalent. Requirements Gives laboratory the ability to provide its own fully formatted report for clinical fidelity. Comments "application/pdf" is recommended as the most reliable and interoperable in this context. Data type Attachment Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` att-1: If the Attachment has data, it SHALL have a contentType `data.empty() or contentType.exists()` Mappings rim: n/a v2: ED/RP rim: ED v2: OBX rim: text (type=ED)

COS version	Profile version	Required COSMIC version	Date	Description
3.0.0	1.0.0	R8.3.05	May 2022	initial version, support for GET

Statuses

FHIR status	Status in COSMIC
PRELIMINARY	PRELIMINARY
ADDITIONAL	APPENDED
FINAL	FINAL
Other	UNKNOWN

ValueSet

The profile includes bindings to the following FHIR defined value set:

ValueSet

id : diagnostic-service-sections

meta

lastUpdated : 2019-11-01T09:29:23.356+11:00

profile : http://hl7.org/fhir/StructureDefinition/shareablevalueset

extension

url : http://hl7.org/fhir/StructureDefinition/structuredefinition-wg

value : oo

extension

url : http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status

value : draft

extension

url : http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm

value : 1

url : http://hl7.org/fhir/ValueSet/diagnostic-service-sections

identifier

system : urn:ietf:rfc:3986

value : urn:oid:2.16.840.1.113883.4.642.3.234

version : 4.0.1

name : DiagnosticServiceSectionCodes

title : Diagnostic Service Section Codes

status : draft

experimental : False

date : 2019-11-01T09:29:23+11:00

publisher : FHIR Project team

contact

telecom

system : url

value : http://hl7.org/fhir

description : This value set includes all the codes in HL7 V2 table 0074.

compose

include

system : http://terminology.hl7.org/CodeSystem/v2-0074

Supported Operations

HTTP Methods

Method	Description
GET	Support for retrieving DiagnosticReport by report ID.

Query Operations

Search Parameters

Parameter	Format	Mandatory	Comment
_profile	string	No
patient	reference	Yes	The subject that the observation is about (if patient). The reference can be a literal reference ex: subject=1 or a Business identifier as well. Ex: subject.identifier=urn:oid:1.2.752.129.2.1.3.1\|20200109-6078
date	date (range)	Yes (to date is optional)	Date format YYYY-MM-DDThh:mm:ss+zz:zz

Supported Queries

GET [baseURL]/DiagnosticReport/[id] (Read)
GET [baseURL]/DiagnosticReport/_search?patient=[]&date=[] (Search)
GET [baseURL]/DiagnosticReport/_search?patient=[]&date=[]&_include=[] (Search)

Supported Operations

Supported SearchInclude Operations

The following searchInclude parameters are supported:

patient
performer
based-on
date

Supported RevInclude Operations

N/A

Error Codes

No specific error codes for DiagnosticReportMicrobiology. For common codes, refer to Error handling section.