@medplum/fhirtypes 0.3.0

package/dist/SubstanceNucleicAcid.d.ts

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+/*
+ * Generated by @medplum/generator
+ * Do not edit manually.
+ */
+
+import { Attachment } from './Attachment';
+import { CodeableConcept } from './CodeableConcept';
+import { Extension } from './Extension';
+import { Identifier } from './Identifier';
+import { Meta } from './Meta';
+import { Narrative } from './Narrative';
+import { Resource } from './Resource';
+
+/**
+ * Nucleic acids are defined by three distinct elements: the base, sugar
+ * and linkage. Individual substance/moiety IDs will be created for each
+ * of these elements. The nucleotide sequence will be always entered in
+ * the 5’-3’ direction.
+ */
+export interface SubstanceNucleicAcid {
+
+  /**
+   * This is a SubstanceNucleicAcid resource
+   */
+  readonly resourceType: 'SubstanceNucleicAcid';
+
+  /**
+   * The logical id of the resource, as used in the URL for the resource.
+   * Once assigned, this value never changes.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly meta?: Meta;
+
+  /**
+   * 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.
+   */
+  readonly implicitRules?: string;
+
+  /**
+   * The base language in which the resource is written.
+   */
+  readonly language?: string;
+
+  /**
+   * 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.
+   */
+  readonly text?: Narrative;
+
+  /**
+   * 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.
+   */
+  readonly contained?: Resource[];
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * 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).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * The type of the sequence shall be specified based on a controlled
+   * vocabulary.
+   */
+  readonly sequenceType?: CodeableConcept;
+
+  /**
+   * The number of linear sequences of nucleotides linked through
+   * phosphodiester bonds shall be described. Subunits would be strands of
+   * nucleic acids that are tightly associated typically through
+   * Watson-Crick base pairing. NOTE: If not specified in the reference
+   * source, the assumption is that there is 1 subunit.
+   */
+  readonly numberOfSubunits?: number;
+
+  /**
+   * The area of hybridisation shall be described if applicable for double
+   * stranded RNA or DNA. The number associated with the subunit followed
+   * by the number associated to the residue shall be specified in
+   * increasing order. The underscore “” shall be used as separator as
+   * follows: “Subunitnumber Residue”.
+   */
+  readonly areaOfHybridisation?: string;
+
+  /**
+   * (TBC).
+   */
+  readonly oligoNucleotideType?: CodeableConcept;
+
+  /**
+   * Subunits are listed in order of decreasing length; sequences of the
+   * same length will be ordered by molecular weight; subunits that have
+   * identical sequences will be repeated multiple times.
+   */
+  readonly subunit?: SubstanceNucleicAcidSubunit[];
+}
+
+/**
+ * Subunits are listed in order of decreasing length; sequences of the
+ * same length will be ordered by molecular weight; subunits that have
+ * identical sequences will be repeated multiple times.
+ */
+export interface SubstanceNucleicAcidSubunit {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * 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).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Index of linear sequences of nucleic acids 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.
+   */
+  readonly subunit?: number;
+
+  /**
+   * Actual nucleotide sequence notation from 5' to 3' end using standard
+   * single letter codes. In addition to the base sequence, sugar and type
+   * of phosphate or non-phosphate linkage should also be captured.
+   */
+  readonly sequence?: string;
+
+  /**
+   * The length of the sequence shall be captured.
+   */
+  readonly length?: number;
+
+  /**
+   * (TBC).
+   */
+  readonly sequenceAttachment?: Attachment;
+
+  /**
+   * The nucleotide present at the 5’ terminal shall be specified based on
+   * a controlled vocabulary. Since the sequence is represented from the 5'
+   * to the 3' end, the 5’ prime nucleotide is the letter at the first
+   * position in the sequence. A separate representation would be
+   * redundant.
+   */
+  readonly fivePrime?: CodeableConcept;
+
+  /**
+   * The nucleotide present at the 3’ terminal shall be specified based on
+   * a controlled vocabulary. Since the sequence is represented from the 5'
+   * to the 3' end, the 5’ prime nucleotide is the letter at the last
+   * position in the sequence. A separate representation would be
+   * redundant.
+   */
+  readonly threePrime?: CodeableConcept;
+
+  /**
+   * The linkages between sugar residues will also be captured.
+   */
+  readonly linkage?: SubstanceNucleicAcidSubunitLinkage[];
+
+  /**
+   * 5.3.6.8.1 Sugar ID (Mandatory).
+   */
+  readonly sugar?: SubstanceNucleicAcidSubunitSugar[];
+}
+
+/**
+ * The linkages between sugar residues will also be captured.
+ */
+export interface SubstanceNucleicAcidSubunitLinkage {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * 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).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * The entity that links the sugar residues together should also be
+   * captured for nearly all naturally occurring nucleic acid the linkage
+   * is a phosphate group. For many synthetic oligonucleotides
+   * phosphorothioate linkages are often seen. Linkage connectivity is
+   * assumed to be 3’-5’. If the linkage is either 3’-3’ or 5’-5’ this
+   * should be specified.
+   */
+  readonly connectivity?: string;
+
+  /**
+   * Each linkage will be registered as a fragment and have an ID.
+   */
+  readonly identifier?: Identifier;
+
+  /**
+   * Each linkage will be registered as a fragment and have at least one
+   * name. A single name shall be assigned to each linkage.
+   */
+  readonly name?: string;
+
+  /**
+   * Residues shall be captured as described in 5.3.6.8.3.
+   */
+  readonly residueSite?: string;
+}
+
+/**
+ * 5.3.6.8.1 Sugar ID (Mandatory).
+ */
+export interface SubstanceNucleicAcidSubunitSugar {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * 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).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * The Substance ID of the sugar or sugar-like component that make up the
+   * nucleotide.
+   */
+  readonly identifier?: Identifier;
+
+  /**
+   * The name of the sugar or sugar-like component that make up the
+   * nucleotide.
+   */
+  readonly name?: string;
+
+  /**
+   * The residues that contain a given sugar will be captured. The order of
+   * given residues will be captured in the 5‘-3‘direction consistent with
+   * the base sequences listed above.
+   */
+  readonly residueSite?: string;
+}