QI-Core Implementation Guide
4.1.0 - release

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## Resource Profile: QICoreSpecimen - Detailed Descriptions

Definitions for the qicore-specimen resource profile.

1. Specimen
Definition | A sample to be used for analysis.
Control | 0..*
Invariants | Defined on this element dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (: contained.contained.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-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-5: If a resource is contained in another resource, it SHALL NOT have a security label (: contained.meta.security.empty()) dom-6: A resource should have narrative for robust management (: text.`div`.exists())
2. Specimen.id
Definition | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
Control | 0..1
Type | string
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.
3. Specimen.meta
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.
Control | 0..1
Type | Meta
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
4. Specimen.implicitRules
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.
Control | 0..1
Type | uri
Is Modifier | true
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.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
5. Specimen.language
Definition | The base language in which the resource is written.
Control | 0..1
Binding | The codes SHOULD be taken from CommonLanguages Max Binding: AllLanguages A human language.
Type | code
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).
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
6. Specimen.text
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.
Control | 0..1
Type | Narrative
Alternate Names | narrative, html, xhtml, display
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.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
7. Specimen.contained
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.
Control | 0..*
Type | Resource
Alternate Names | inline resources, anonymous resources, contained resources
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.
8. Specimen.extension
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.
Control | 0..*
Type | Extension
Alternate Names | extensions, user content
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.
Invariants | Defined on this element 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())
9. Specimen.modifierExtension
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).
Control | 0..*
Type | Extension
Is Modifier | true
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.
Alternate Names | extensions, user content
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.
Invariants | Defined on this element 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())
10. Specimen.identifier
Definition | Id for specimen.
Note | This is a business identifier, not a resource identifier (see discussion)
Control | 0..*
Type | Identifier
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
11. Specimen.accessionIdentifier
Definition | The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.
Control | 0..1
Type | Identifier
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
12. Specimen.status
Definition | The availability of the specimen.
Control | 0..1
Binding | The codes SHALL be taken from SpecimenStatus Codes providing the status/availability of a specimen.
Type | code
Is Modifier | true
Comments | This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
13. Specimen.type
Definition | The kind of material that forms the specimen.
Control | 0..1
Binding | For example codes, see hl7VS-specimenType The type of the specimen.
Type | CodeableConcept
Must Support | true
Comments | The type can change the way that a specimen is handled and drives what kind of analyses can properly be performed on the specimen. It is frequently used in diagnostic work flow decision making systems.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
14. Specimen.subject
Definition | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device.
Control | 0..1
Type | Reference(QICorePatient | QICoreDevice | QICoreSubstance | Group)
Must Support | true
Must Support Types | No must-support rules about the choice of types/profiles
Requirements | Must know the subject context.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
15. Specimen.receivedTime
Definition | Time when specimen was received for processing or testing.
Control | 0..1
Type | dateTime
Must Support | true
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
16. Specimen.parent
Definition | Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.
Control | 0..*
Type | Reference(QICoreSpecimen)
Comments | The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
17. Specimen.request
Definition | Details concerning a service request that required a specimen to be collected.
Control | 0..*
Type | Reference(ServiceRequest)
Comments | The request may be explicit or implied such with a ServiceRequest that requires a blood draw.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
18. Specimen.collection
Definition | Details concerning the specimen collection.
Control | 0..1
Type | BackboneElement
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
19. Specimen.collection.id
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Control | 0..1
Type | string
20. Specimen.collection.extension
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.
Control | 0..*
Type | Extension
Alternate Names | extensions, user content
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.
Invariants | Defined on this element 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())
21. Specimen.collection.modifierExtension
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained 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 can 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).
Control | 0..*
Type | Extension
Is Modifier | true
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.
Alternate Names | extensions, user content, modifiers
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.
Invariants | Defined on this element 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())
22. Specimen.collection.collector
Definition | Person who collected the specimen.
Control | 0..1
Type | Reference(QICorePractitioner)
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
23. Specimen.collection.collected[x]
Definition | Time when specimen was collected from subject - the physiologically relevant time.
Control | 0..1
Type | Choice of: dateTime, Period
[x] Note | See Choice of Data Types for further information about how to use [x]
Must Support | true
Must Support Types | No must-support rules about the choice of types/profiles
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
24. Specimen.collection.duration
Definition | The span of time over which the collection of a specimen occurred.
Control | 0..1
Type | Duration
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
25. Specimen.collection.quantity
Definition | The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.
Control | 0..1
Type | Quantity(SimpleQuantity)
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
26. Specimen.collection.method
Definition | A coded value specifying the technique that is used to perform the procedure.
Control | 0..1
Binding | For example codes, see FHIRSpecimenCollectionMethod The technique that is used to perform the procedure.
Type | CodeableConcept
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
27. Specimen.collection.bodySite
Definition | Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens.
Control | 0..1
Binding | For example codes, see SNOMEDCTBodyStructures Codes describing anatomical locations. May include laterality.
Type | CodeableConcept
Must Support | true
Comments | If the use case requires BodySite to be handled as a separate resource instead of an inline coded element (e.g. to identify and track separately) then use the standard extension bodySite.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
28. Specimen.collection.fastingStatus[x]
Definition | Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.
Control | 0..1
Binding | The codes SHALL be taken from hl7VS-relevantClincialInformation; other codes may be used where these codes are not suitable Codes describing the fasting status of the patient.
Type | Choice of: CodeableConcept, Duration
[x] Note | See Choice of Data Types for further information about how to use [x]
Requirements | Many diagnostic tests require fasting to facilitate accurate interpretation.
Comments | Representing fasting status using this element is preferred to representing it with an observation using a 'pre-coordinated code' such as LOINC 2005-7 (Calcium [Moles/​time] in 2 hour Urine --12 hours fasting), or using a component observation `such as`Observation.component code` = LOINC 49541-6 (Fasting status - Reported).
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
29. Specimen.processing
Definition | Details concerning processing and processing steps for the specimen.
Control | 0..*
Type | BackboneElement
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
30. Specimen.processing.id
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Control | 0..1
Type | string
31. Specimen.processing.extension
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.
Control | 0..*
Type | Extension
Alternate Names | extensions, user content
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.
Invariants | Defined on this element 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())
32. Specimen.processing.modifierExtension
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained 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 can 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).
Control | 0..*
Type | Extension
Is Modifier | true
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.
Alternate Names | extensions, user content, modifiers
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.
Invariants | Defined on this element 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())
33. Specimen.processing.description
Definition | Textual description of procedure.
Control | 0..1
Type | string
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
34. Specimen.processing.procedure
Definition | A coded value specifying the procedure used to process the specimen.
Control | 0..1
Binding | For example codes, see SpecimenProcessingProcedure Type indicating the technique used to process the specimen.
Type | CodeableConcept
Must Support | true
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
35. Specimen.processing.additive
Definition | Material used in the processing step.
Control | 0..*
Type | Reference(QICoreSubstance)
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
36. Specimen.processing.time[x]
Definition | A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalin.
Control | 0..1
Type | Choice of: dateTime, Period
[x] Note | See Choice of Data Types for further information about how to use [x]
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
37. Specimen.container
Definition | The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.
Control | 0..*
Type | BackboneElement
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
38. Specimen.container.id
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Control | 0..1
Type | string
39. Specimen.container.extension
Definition | An Extension
Control | 0..*
Type | Extension
Invariants | Defined on this element 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())
Slicing | This element introduces a set of slices on Specimen.container.extension. The slices are unordered and Open, and can be differentiated using the following discriminators: value @ url
40. Specimen.container.extension:container-sequenceNumber
SliceName | container-sequenceNumber
Definition | An assigned number on the specimen denoting the order of collection.
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(sequenceNumber) (Extension Type: integer)
Invariants | Defined on this element 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())
41. Specimen.container.modifierExtension
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained 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 can 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).
Control | 0..*
Type | Extension
Is Modifier | true
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.
Alternate Names | extensions, user content, modifiers
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.
Invariants | Defined on this element 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())
42. Specimen.container.identifier
Definition | Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances.
Note | This is a business identifier, not a resource identifier (see discussion)
Control | 0..*
Type | Identifier
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
43. Specimen.container.description
Definition | Textual description of the container.
Control | 0..1
Type | string
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
44. Specimen.container.type
Definition | The type of container associated with the specimen (e.g. slide, aliquot, etc.).
Control | 0..1
Binding | For example codes, see SpecimenContainerType Type of specimen container.
Type | CodeableConcept
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
45. Specimen.container.capacity
Definition | The capacity (volume or other measure) the container may contain.
Control | 0..1
Type | Quantity(SimpleQuantity)
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
46. Specimen.container.specimenQuantity
Definition | The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.
Control | 0..1
Type | Quantity(SimpleQuantity)
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
47. Specimen.container.additive[x]
Definition | Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.
Control | 0..1
Binding | For example codes, see hl7VS-additivePreservative Substance added to specimen container.
Type | Choice of: CodeableConcept, Reference(QICoreSubstance)
[x] Note | See Choice of Data Types for further information about how to use [x]
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
48. Specimen.condition
Definition | A mode or state of being that describes the nature of the specimen.
Control | 0..*
Binding | The codes SHALL be taken from hl7VS-specimenCondition; other codes may be used where these codes are not suitable Codes describing the state of the specimen.
Type | CodeableConcept
Requirements | The specimen condition can be used to assess its quality or appropriateness for a specific test.
Comments | Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess its quality or appropriateness for a specific test.
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
49. Specimen.note
Definition | To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).
Control | 0..*
Type | Annotation
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))