StructureDefinition
An
example
of
a
herd
screening
ELISA
assay
for
substanceprotein
Mycoplasmal
Pneumonia
in
Pigs.
(id
=
"herd1")
{
"resourceType" : "StructureDefinition",
"id" : "SubstanceProtein",
"meta" : {
"lastUpdated" : "2019-11-01T09:29:23.356+11:00"
},
"text" : {
"status" : "generated",
"div" : "<div>!-- Snipped for Brevity --></div>"
},
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-category",
"valueString" : "Specialized.Medication Definition"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode" : "trial-use"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger" : 0
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category",
"valueCode" : "anonymous"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "brr"
}],
"url" : "http://hl7.org/fhir/StructureDefinition/SubstanceProtein",
"version" : "4.0.1",
"name" : "SubstanceProtein",
"status" : "draft",
"date" : "2019-11-01T09:29:23+11:00",
"publisher" : "Health Level Seven International (Biomedical Research and Regulation)",
"contact" : [{
"telecom" : [{
"system" : "url",
"value" : "http://hl7.org/fhir"
}]
},
{
"telecom" : [{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/rcrim/index.cfm"
}]
}],
"description" : "A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators.",
"fhirVersion" : "4.0.1",
"mapping" : [{
"identity" : "rim",
"uri" : "http://hl7.org/v3",
"name" : "RIM Mapping"
}],
"kind" : "resource",
"abstract" : false,
"type" : "SubstanceProtein",
"baseDefinition" : "http://hl7.org/fhir/StructureDefinition/DomainResource",
"derivation" : "specialization",
"snapshot" : {
"element" : [{
"id" : "SubstanceProtein",
"path" : "SubstanceProtein",
"short" : "A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators",
"definition" : "A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators.",
"min" : 0,
"max" : "*",
"base" : {
"path" : "SubstanceProtein",
"min" : 0,
"max" : "*"
},
"constraint" : [{
"key" : "dom-2",
"severity" : "error",
"human" : "If the resource is contained in another resource, it SHALL NOT contain nested Resources",
"expression" : "contained.contained.empty()",
"xpath" : "not(parent::f:contained and f:contained)",
"source" : "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key" : "dom-3",
"severity" : "error",
"human" : "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",
"expression" : "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()",
"xpath" : "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))",
"source" : "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key" : "dom-4",
"severity" : "error",
"human" : "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated",
"expression" : "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()",
"xpath" : "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))",
"source" : "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key" : "dom-5",
"severity" : "error",
"human" : "If a resource is contained in another resource, it SHALL NOT have a security label",
"expression" : "contained.meta.security.empty()",
"xpath" : "not(exists(f:contained/*/f:meta/f:security))",
"source" : "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice",
"valueBoolean" : true
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation",
"valueMarkdown" : "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time."
}],
"key" : "dom-6",
"severity" : "warning",
"human" : "A resource should have narrative for robust management",
"expression" : "text.`div`.exists()",
"xpath" : "exists(f:text/h:div)",
"source" : "http://hl7.org/fhir/StructureDefinition/DomainResource"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "Entity. Role, or Act"
}]
},
{
"id" : "SubstanceProtein.id",
"path" : "SubstanceProtein.id",
"short" : "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.",
"comment" : "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Resource.id",
"min" : 0,
"max" : "1"
},
"type" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}],
"code" : "http://hl7.org/fhirpath/System.String"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.meta",
"path" : "SubstanceProtein.meta",
"short" : "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.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Resource.meta",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "Meta"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.implicitRules",
"path" : "SubstanceProtein.implicitRules",
"short" : "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.",
"comment" : "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.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Resource.implicitRules",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "uri"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : true,
"isModifierReason" : "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation",
"isSummary" : true
},
{
"id" : "SubstanceProtein.language",
"path" : "SubstanceProtein.language",
"short" : "Language of the resource content",
"definition" : "The base language in which the resource is written.",
"comment" : "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).",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Resource.language",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "code"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : false,
"binding" : {
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
"valueCanonical" : "http://hl7.org/fhir/ValueSet/all-languages"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString" : "Language"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding",
"valueBoolean" : true
}],
"strength" : "preferred",
"description" : "A human language.",
"valueSet" : "http://hl7.org/fhir/ValueSet/languages"
}
},
{
"id" : "SubstanceProtein.text",
"path" : "SubstanceProtein.text",
"short" : "Text summary of the resource, for human interpretation",
"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.",
"comment" : "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.",
"alias" : ["narrative",
"html",
"xhtml",
"display"],
"min" : 0,
"max" : "1",
"base" : {
"path" : "DomainResource.text",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "Narrative"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "Act.text?"
}]
},
{
"id" : "SubstanceProtein.contained",
"path" : "SubstanceProtein.contained",
"short" : "Contained, inline 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.",
"comment" : "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.",
"alias" : ["inline resources",
"anonymous resources",
"contained resources"],
"min" : 0,
"max" : "*",
"base" : {
"path" : "DomainResource.contained",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "Resource"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "N/A"
}]
},
{
"id" : "SubstanceProtein.extension",
"path" : "SubstanceProtein.extension",
"short" : "Additional content defined by implementations",
"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.",
"comment" : "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.",
"alias" : ["extensions",
"user content"],
"min" : 0,
"max" : "*",
"base" : {
"path" : "DomainResource.extension",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "Extension"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "N/A"
}]
},
{
"id" : "SubstanceProtein.modifierExtension",
"path" : "SubstanceProtein.modifierExtension",
"short" : "Extensions that cannot be ignored",
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"comment" : "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.",
"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](extensibility.html#modifierExtension).",
"alias" : ["extensions",
"user content"],
"min" : 0,
"max" : "*",
"base" : {
"path" : "DomainResource.modifierExtension",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "Extension"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}],
"isModifier" : true,
"isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them",
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "N/A"
}]
},
{
"id" : "SubstanceProtein.sequenceType",
"path" : "SubstanceProtein.sequenceType",
"short" : "The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence",
"definition" : "The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.sequenceType",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "CodeableConcept"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.numberOfSubunits",
"path" : "SubstanceProtein.numberOfSubunits",
"short" : "Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable",
"definition" : "Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.numberOfSubunits",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "integer"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.disulfideLinkage",
"path" : "SubstanceProtein.disulfideLinkage",
"short" : "The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions",
"definition" : "The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions.",
"min" : 0,
"max" : "*",
"base" : {
"path" : "SubstanceProtein.disulfideLinkage",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "string"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit",
"path" : "SubstanceProtein.subunit",
"short" : "This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times",
"definition" : "This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.",
"min" : 0,
"max" : "*",
"base" : {
"path" : "SubstanceProtein.subunit",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "BackboneElement"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.id",
"path" : "SubstanceProtein.subunit.id",
"representation" : ["xmlAttr"],
"short" : "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.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}],
"code" : "http://hl7.org/fhirpath/System.String"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "n/a"
}]
},
{
"id" : "SubstanceProtein.subunit.extension",
"path" : "SubstanceProtein.subunit.extension",
"short" : "Additional content defined by implementations",
"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.",
"comment" : "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.",
"alias" : ["extensions",
"user content"],
"min" : 0,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "Extension"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}],
"isModifier" : false,
"isSummary" : false,
"mapping" : [{
"identity" : "rim",
"map" : "n/a"
}]
},
{
"id" : "SubstanceProtein.subunit.modifierExtension",
"path" : "SubstanceProtein.subunit.modifierExtension",
"short" : "Extensions that cannot be ignored even if unrecognized",
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"comment" : "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.",
"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](extensibility.html#modifierExtension).",
"alias" : ["extensions",
"user content",
"modifiers"],
"min" : 0,
"max" : "*",
"base" : {
"path" : "BackboneElement.modifierExtension",
"min" : 0,
"max" : "*"
},
"type" : [{
"code" : "Extension"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}],
"isModifier" : true,
"isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary" : true,
"mapping" : [{
"identity" : "rim",
"map" : "N/A"
}]
},
{
"id" : "SubstanceProtein.subunit.subunit",
"path" : "SubstanceProtein.subunit.subunit",
"short" : "Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts",
"definition" : "Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.subunit",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "integer"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.sequence",
"path" : "SubstanceProtein.subunit.sequence",
"short" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence",
"definition" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.sequence",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "string"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.length",
"path" : "SubstanceProtein.subunit.length",
"short" : "Length of linear sequences of amino acids contained in the subunit",
"definition" : "Length of linear sequences of amino acids contained in the subunit.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.length",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "integer"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.sequenceAttachment",
"path" : "SubstanceProtein.subunit.sequenceAttachment",
"short" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence",
"definition" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.sequenceAttachment",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "Attachment"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.nTerminalModificationId",
"path" : "SubstanceProtein.subunit.nTerminalModificationId",
"short" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID",
"definition" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.nTerminalModificationId",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "Identifier"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.nTerminalModification",
"path" : "SubstanceProtein.subunit.nTerminalModification",
"short" : "The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified",
"definition" : "The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.nTerminalModification",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "string"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.cTerminalModificationId",
"path" : "SubstanceProtein.subunit.cTerminalModificationId",
"short" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID",
"definition" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.cTerminalModificationId",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "Identifier"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.cTerminalModification",
"path" : "SubstanceProtein.subunit.cTerminalModification",
"short" : "The modification at the C-terminal shall be specified",
"definition" : "The modification at the C-terminal shall be specified.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "SubstanceProtein.subunit.cTerminalModification",
"min" : 0,
"max" : "1"
},
"type" : [{
"code" : "string"
}],
"constraint" : [{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}],
"isModifier" : false,
"isSummary" : true
}]
},
"differential" : {
"element" : [{
"id" : "SubstanceProtein",
"path" : "SubstanceProtein",
"short" : "A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators",
"definition" : "A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators.",
"min" : 0,
"max" : "*"
},
{
"id" : "SubstanceProtein.sequenceType",
"path" : "SubstanceProtein.sequenceType",
"short" : "The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence",
"definition" : "The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "CodeableConcept"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.numberOfSubunits",
"path" : "SubstanceProtein.numberOfSubunits",
"short" : "Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable",
"definition" : "Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "integer"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.disulfideLinkage",
"path" : "SubstanceProtein.disulfideLinkage",
"short" : "The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions",
"definition" : "The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions.",
"min" : 0,
"max" : "*",
"type" : [{
"code" : "string"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit",
"path" : "SubstanceProtein.subunit",
"short" : "This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times",
"definition" : "This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.",
"min" : 0,
"max" : "*",
"type" : [{
"code" : "BackboneElement"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.subunit",
"path" : "SubstanceProtein.subunit.subunit",
"short" : "Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts",
"definition" : "Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "integer"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.sequence",
"path" : "SubstanceProtein.subunit.sequence",
"short" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence",
"definition" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "string"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.length",
"path" : "SubstanceProtein.subunit.length",
"short" : "Length of linear sequences of amino acids contained in the subunit",
"definition" : "Length of linear sequences of amino acids contained in the subunit.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "integer"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.sequenceAttachment",
"path" : "SubstanceProtein.subunit.sequenceAttachment",
"short" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence",
"definition" : "The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "Attachment"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.nTerminalModificationId",
"path" : "SubstanceProtein.subunit.nTerminalModificationId",
"short" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID",
"definition" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "Identifier"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.nTerminalModification",
"path" : "SubstanceProtein.subunit.nTerminalModification",
"short" : "The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified",
"definition" : "The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "string"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.cTerminalModificationId",
"path" : "SubstanceProtein.subunit.cTerminalModificationId",
"short" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID",
"definition" : "Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "Identifier"
}],
"isSummary" : true
},
{
"id" : "SubstanceProtein.subunit.cTerminalModification",
"path" : "SubstanceProtein.subunit.cTerminalModification",
"short" : "The modification at the C-terminal shall be specified",
"definition" : "The modification at the C-terminal shall be specified.",
"min" : 0,
"max" : "1",
"type" : [{
"code" : "string"
}],
"isSummary" : true
}]
}
}
<?xml version="1.0" encoding="UTF-8"?>
<Observation xmlns="http://hl7.org/fhir">
<id value="herd1"/>
<text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative: Observation</b> <a name="herd1"> </a> </p> <div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border:
1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource Observation "herd1" </p> </div> <p> <b> status</b> : <span title=" the mandatory status ">final</span> </p> <p> <b> category</b> : <span title=" category code is A code that classifies the general type of observation being
made. This is used for searching, sorting and display purposes. ">Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a> #laboratory)</span> </span> </p> <p> <b> code</b> : <span title="
Observations are often coded in multiple code systems.
- LOINC provides codes of varying granularity (though not usefully more specific
in this particular case) and more generic LOINCs can be mapped to more specific
codes as shown here
- snomed provides a clinically relevant code that is usually less granular
than LOINC
- the source system provides its own code, which may be less or more granular
than LOINC
">Mycoplasma hyopneumoniae - MHP <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a> #80219-9 "Mycoplasma hyopneumoniae Ab sample/Positive control in Serum by
Immunoassay"; clinical-codes#Mycoplasma "Mycoplasma")</span> </span> </p> <p> <b> subject</b> : <span title=" subject is a herd of 2500 breding sows "><a href="group-example-herd1.html">Group/herd1</a> "Breeding herd"</span> </p> <p> <b> encounter</b> : <span> : part of a health assurance program</span> </p> <p> <b> effective</b> : 2017-11-20</p> <p> <b> value</b> : <span title=" In FHIR, units may be represented twice. Once in the
agreed human representation, and once in a coded form.
Both is best, since it's not always possible to infer
one from the other in code.
When a computable unit is provided, UCUM (http://unitsofmeasure.org)
is always preferred, but it doesn't provide notional units (such as
"tablet"), etc. For these, something else is required (e.g. SNOMED
CT)
">0.2 % (sample/positive control)<span style="background: LightGoldenRodYellow"> (Details: UCUM code % = '%')</span> </span> </p> <p> <b> interpretation</b> : Negative <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ObservationInterpretation.html">ObservationInterpretation</a> #NEG)</span> </p> <p> <b> specimen</b> : <span title=" Specimen is a pooled serology sample of 30 animals. "><a href="specimen-example-pooled-serum.html">Specimen/pooled-serum: 30 serum</a> </span> </p> <h3> ReferenceRanges</h3> <table class="grid"><tr> <td> -</td> <td> <b> Text</b> </td> </tr> <tr> <td> *</td> <td> >0.4 Positive; 0.3 to 0.4 Suspect < 0.3 Negative</td> </tr> </table> </div> </text> <status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
<display value="Laboratory"/>
</coding>
<text value="Laboratory"/>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="80219-9"/>
<display value="Mycoplasma hyopneumoniae Ab sample/Positive control in Serum by Immunoassay"/>
</coding>
<coding>
<system value="http://acme.org/devices/clinical-codes"/>
<code value="Mycoplasma"/>
<display value="Mycoplasma"/>
</coding>
<text value="Mycoplasma hyopneumoniae - MHP"/>
</code>
<subject>
<reference value="Group/herd1"/>
</subject>
<encounter>
<display value="part of a health assurance program"/>
</encounter>
<effectiveDateTime value="2017-11-20"/>
<valueQuantity>
<value value="0.2"/>
<unit value="% (sample/positive control)"/>
<system value="http://unitsofmeasure.org"/>
<code value="%"/>
</valueQuantity>
<interpretation>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"/>
<code value="NEG"/>
<display value="Negative"/>
</coding>
<text value="Negative"/>
</interpretation>
<specimen>
<reference value="Specimen/pooled-serum"/>
<display value="30 serum"/>
</specimen>
<referenceRange>
<text value=">0.4 Positive; 0.3 to 0.4 Suspect < 0.3 Negative"/>
</referenceRange>
</
Observation
>
Usage
note:
every
effort
has
been
made
to
ensure
that
the
examples
are
correct
and
useful,
but
they
are
not
a
normative
part
of
the
specification.
Diagnostics
.
Page
versions:
R5
R4B
R4
|
Propose
a
change