Ballot to Master STU2

input-cache/workgroups.xml

@@ -24,7 +24,8 @@
   <workgroup key="dev" webcode="healthcaredevices" name="Devices" listserv="[email protected]/"/>
   <workgroup key="ec" webcode="ec" name="Emergency Care" listserv="[email protected]/"/>
   <workgroup key="ehr" webcode="ehr" name="Electronic Health Record" listserv="[email protected]/"/>
-  <workgroup key="director" name="FHIR Director"/>
+  <workgroup key="ex" webcode="ec" name="Executive Committee" listserv="[email protected]/"/>
+  <workgroup key="director" name="FHIR Director" listserv="[email protected]"/>
   <workgroup key="fgb" name="FHIR Governance Board" deprecated="true"/>
   <workgroup key="fhir-i" webcode="fiwg" name="FHIR Infrastructure" listserv="[email protected]/"/>
   <workgroup key="fmg" webcode="fhirmg" name="FHIR Mgmt Group" listserv="[email protected]/"/>

input/fsh/CommonOrganization.fsh

@@ -1,7 +1,6 @@
 RuleSet: DUNSandFEINumber
 * identifier 1..* MS
 * identifier.type 0..1 MS
-* identifier.type from PqcmcOrgIdentifierTypeTerminology (required)
 * identifier.system 1..1 MS
 * identifier.value 1..1 MS
 * identifier ^slicing.discriminator.type = #value

input/fsh/DrugSubstanceResources.fsh

@@ -563,6 +563,134 @@ RuleSet: CountryOfOrigin
 
 //*Stage 2 --------------------------------------------------------------------------------------------------------------*/
 
+Profile: DrugSubstanceCharacterisation
+Parent: SubstanceDefinition
+Id: pqcmc-drug-substance-characterisation
+Title: "Drug Substance"
+Description: "Drug Substance (Active Ingredient) nomenclature and characterisation."
+* . obeys cmc-when-unii-required
+* . obeys cmc-name-isbt
+* obeys cmc-substance-characterisation-content-required
+* identifier 0..1 MS
+* identifier ^short = "optional user designated identifier"
+* classification 1..1 MS
+* classification from SubstanceClassification
+* classification ^short = "Substance Type"
+* classification ^definition = """A controlled vocabulary as provided by the prEN ISO 11238 - Health informatics identification of medicinal products - Structures and controlled vocabularies for drug substances to group drug substances at a relatively high level acording to the Substance and the Substance Preparation Model.
+[Source: Adapted from 'Logical model of the classification and identification of pharmaceutical and medicinal Products', HL7]
+"""
+* manufacturer 0..1 MS
+* insert PQReference(manufacturer)
+* manufacturer only Reference(CodedOrganization)
+* supplier 0..1 MS
+* insert PQReference(supplier)
+* supplier only Reference(CodedOrganization)
+* insert SubstanceCharacterization
+* insert UniiAndUniProtCodes(1)
+* insert ShortSetSubstanceNames
+
+* relationship 0..* MS
+  * ^short = "Reference to Drug Substance Impurity"
+//* relationship obeys cmc-substance-relationship  not needed  since this resource is for illustraion.
+  * substanceDefinition[x] 1..1 MS
+  * insert PQReference(substanceDefinition[x])
+  * substanceDefinition[x] only Reference(ImpuritySubstance)
+
+Profile: ImpuritySubstance
+Parent: SubstanceDefinition
+Id: pqcmc-drug-product-substance-impurity
+Title: "Drug Substance Impurity"
+Description: "Any component of the drug substance that is not the chemical entity for procduct composition."
+* obeys cmc-impurity-unii-required
+* identifier 0..1 MS
+* identifier ^short = "optional user designated identifier"
+* classification 1..* MS
+* classification from PqcmcImpurityClassificationTerminology (required)
+* classification ^short = "Impurity Classification"
+* classification ^definition = """A categorization of impurities based on its origin. [Source: SME Defined]
+Examples: Degradation Product, Inorganic, Process Related/Process, Product Related, Leachables.
+"""
+* insert SubstanceCharacterization
+* structure 0..1 MS
+//* structure obeys cmc-representation-or-document
+* structure.technique MS
+* structure.technique ^short = "Impurity Substance Characterisation Technique"
+* structure.technique ^definition = """The technique used to elucidate the structure or characterisation of the drug substance. [Source: SME Defined] Examples: x-ray, HPLC, NMR, peptide mapping, ligand binding assay.
+"""
+* structure.technique only CodeableConceptTextOnly
+* structure
+  * representation MS
+    * ^short = "Impurity Structure Graphic | Impurity Structure Data File"
+    * ^slicing.discriminator.type = #value
+    * ^slicing.rules = #closed
+    * ^slicing.discriminator.path = "type"
+    * ^slicing.ordered = false
+    * type 1..1 MS
+    * type from PqcmcRepresentationTypes (required)
+  * representation contains
+    graphic 0..1 and
+    structureFile 0..* and
+    structureString 0..*
+  * representation[graphic]
+    * ^short = "A graphical, displayable depiction of the structure (e.g. an SVG, PNG)"
+    * type 1..1 MS
+      * ^short = "Graphic"
+    * type = $NCIT#C54273
+    * document 1..1
+      * ^short = "Impurity Structure Graphic"
+      * ^definition = """
+        A pictorial representation of the structure of the impurity substance. 
+        [Source: SME Defined] Note: Refer to the 'Acceptable File Formats for 
+        use in eCTD' Example: This is the representation of the molecule CH3OH, 
+        or the sequence SHLVEALALVAGERG.
+      """
+    * insert PQReference(document)
+    * document only Reference(GraphicReference)
+  * representation[structureFile]
+    * ^short = "machine-readable representation -- attached file"
+    * type 1..1 MS
+      * ^short = "Structure File"
+    * type = $NCIT#C103240
+    * document 1..1 MS
+      * ^short = "Impurity Chemical Structure Data (files, e.g. .SDF, .CIF)"
+    * insert PQReference(document)
+    * document only Reference(StructureReference)
+  * representation[structureString]
+    * ^short = "machine-readable representation -- plain text"
+    * type 1..1 MS
+      * ^short = "Structure Textual"
+    * type = $NCIT#C45253
+    * format 1..1 MS
+      * ^short = "Drug Substance Impurity Method Type"
+    * format from PqcmcChemicalStructureDataFileTypeTerminology (required)
+    * representation 1..1 MS
+      * ^short = "Impurity Chemical Structure Data (short, plain text representations, e.g. SMILES)"
+      * ^definition = """
+        A machine-readable representation of the structure of the chemical. [Source: SME Defined]
+        Examples: SMILES, INCHI
+      """
+//   * representation[structureData]
+//     * ^short = "machine-readable representation -- may be plain text (e.g. SMILES) or an attached file (e.g. SDF)"
+//     * format 0..1 MS
+//     * format ^short = "Drug Substance Impurity Method Type"
+//     * format.text 0..1 MS
+//     * type 1..1 MS
+//       * text 1..1 MS
+//       * text = "Structure"
+//     * representation 0..1 MS
+//     * representation ^short = "Impurity Chemical Structure Data (short, plain text representations, e.g. SMILES)"
+//     * representation ^definition = """A machine-readable representation of the structure of the chemical. [Source: SME Defined]
+// Examples: Structured Data File (SDF), MOLFILE, InChI file (small molecule), PDB, mmCIF (large molecules), HELM.
+// """
+//     * document 0..1 MS
+//     * document ^short = "Impurity Chemical Structure Data (large files, e.g. SDF, CIF)"
+//     * document only Reference(StructureReference)
+
+// impurities might be unknown and not have Unii's
+* insert UniiAndUniProtCodes(0)
+* insert ShortSetSubstanceNames
+* insert CompanyName
+
 //Rulesets---------------------------------------------------------------------------------------------------------------*/
 RuleSet: SubstanceCharacterization
 * characterization MS
@@ -594,6 +722,40 @@ Example: This is the representation of the instrumental output for the molecule
     * ^definition = """Impurity Analytical Instrument Data File: The transport format for data exchange. [Source: SME Defined]
 Example: JCAMP, ADX, ADF."""
 
+Profile: DrugProductIngredient
+Parent: Ingredient
+Id: pqcmc-dp-ingredient
+Title: "Drug Product Batch Formula Ingredient"
+Description: "The amount details about the drug product ingredients in the batch. Use for Batch Formula."
+
+* identifier 0..1 MS
+* substance.code 1..1 MS
+* substance.code ^short = "Ingredient Substance"
+* insert PQCodeableReference(substance.code)
+* substance.code only CodeableReference(pqcmc-routine-drug-substance or pqcmc-excipient)
+* substance
+  * strength 2..2 MS
+    * ^slicing.discriminator.type = #value
+    * ^slicing.rules = #closed
+    * ^slicing.discriminator.path = "concentration.code"
+    * ^slicing.ordered = false
+  * strength contains 
+    perBatch 1..1 MS and
+    percent 1..1 MS
+  * strength[perBatch]
+    * ^short = "Ingredient Total per Batch"
+    * ^definition = "the total amount of thi ingredient present in the batch"
+    * concentration[x] 1..1 MS
+    * concentration[x] only Quantity
+    * concentrationQuantity.code 1..1 MS
+    * concentrationQuantity.code from PqcmcNonPercentageUnits (required)
+  * strength[percent]
+    * ^short = "Ingredient percent of Total Batch"
+    * concentration[x] 1..1 MS
+    * concentration[x] only Quantity
+    * concentrationQuantity.code 1..1 MS
+    * concentrationQuantity.code from PqcmcPercentageUnits (required)
+
 
 RuleSet: GraphicAndStructureRepresentations(graphicsCardinality, structureFileCardinality,structureStringCardinality)
 * structure

input/fsh/HierarchySupplement.fsh

@@ -0,0 +1,142 @@
+RuleSet: child(parent,child)
+* {parent}
+  * ^property[+].code = #child
+  * ^property[=].valueCode = {child}
+
+CodeSystem: NCItHierarchySupplement
+Id: cmc-hierarchy-supplement
+Title: "PQ-CMC-FDA NCIt Hieararchy Supplement"
+Description: """Provides hierarchical relationships for value sets as a CodeSystem supplement to the NCI Thesaurus (NCIt) """
+* ^experimental = false
+* ^status = #draft
+* ^publisher = "NCI Thesaurus (NCIt)"
+* ^copyright = "PQ-CMC-FDA Temporary Codes are either in the NCI Thesaurus (NCIt) or are in the process of being included in NCIt. When all codes are in NCIt, they will migrate to the HL7 Terminology (THO). License Note Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source. For more licensing information see: [https://www.cancer.gov/policies/copyright-reuse](https://www.cancer.gov/policies/copyright-reuse)"
+* ^supplements = Canonical(http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl)
+* ^content = #supplement
+* ^property[+].code = #child
+* ^hierarchyMeaning = #is-a
+// uri MUST be in quotes or it won't work
+* ^property[=].uri = "http://hl7.org/fhir/concept-properties#child"
+* ^property[=].description = "Defines which codes are children"
+* ^property[=].type = #code
+// * #C60819
+* insert child(#C60819,#C204845)
+* insert child(#C60819,#C205001)
+* insert child(#C60819,#C81183)
+* insert child(#C60819,#C205003)
+* insert child(#C60819,#C205007)
+* insert child(#C60819,#C205015)
+* insert child(#C60819,#C205018)
+* insert child(#C60819,#C205020)
+* insert child(#C60819,#C205028)
+* insert child(#C60819,#C62352)
+* insert child(#C60819,#C171277)
+* insert child(#C60819,#C205038)
+* insert child(#C60819,#C64858)
+* insert child(#C60819,#C205006)
+//* #C134249
+// * #C134250
+* insert child(#C134250,#C205004)
+* insert child(#C134250,#C205019)
+* insert child(#C134250,#C134115)
+* insert child(#C134250,#C205050)
+// * #C133961
+// * #C205026
+* insert child(#C205026,#C138990)
+* insert child(#C205026,#C139027)
+* insert child(#C205026,#C134262)
+* insert child(#C205026,#C134261)
+// * #C138993
+// * #C134252
+// * #C134253
+// * #C205012
+// * #C193381
+* insert child(#C193381,#C205024) 
+// * #C134255
+// * #C134256
+// * #C205027
+// * #C134257
+// * #C134260
+// * #C134263
+// * #C133974
+// * #C133975
+// * #C134264
+// * #C63394
+// * #C103201
+// * #C205029
+// * #C60821
+// * #C64832
+// * #C25483
+* insert child(#C25483,#C205022)
+* insert child(#C25483,#C205017)
+* insert child(#C25483,#C205209)
+* insert child(#C25483,#C205053)
+* insert child(#C25483,#C205021)
+* insert child(#C25483,#C205016)
+* insert child(#C25483,#C205206)
+* insert child(#C25483,#C205045)
+* insert child(#C25483,#C205036)
+* insert child(#C25483,#C205011)
+* insert child(#C25483,#C205010)
+* insert child(#C25483,#C205009)
+* insert child(#C25483,#C205037)
+* insert child(#C25483,#C205025)
+* insert child(#C25483,#C205034)
+* insert child(#C25483,#C205033)
+* insert child(#C25483,#C205035)
+* insert child(#C25483,#C205005)
+* insert child(#C25483,#C205044)
+* insert child(#C25483,#C205043)
+* insert child(#C25483,#C205042)
+// * #C134266
+// * #C205049
+// * #C133979
+// * #C134267
+// * #C134269
+// * #C205030
+// * #C134270
+// * #C133983
+// * #C134272
+// * #C133985
+// * #C205032
+// * #C134276
+// * #C134277
+// * #C134278
+// * #C134113
+// * #C134114
+// * #C200004
+// * #C205023
+// * #C205041
+// * #C18951
+* insert child(#C18951,#C16643)
+* insert child(#C18951,#C205054)
+* insert child(#C18951,#C205031)
+* insert child(#C18951,#C205002)
+* insert child(#C18951,#C205008)
+// * #C205000
+// * #C205013
+// * #C74723
+// * #C204971
+* insert child(#C204971,#C205039)
+* insert child(#C204971,#C205040)
+* insert child(#C204971,#C205052)
+* insert child(#C204971,#C205047)
+* insert child(#C204971,#C205048)
+* insert child(#C204971,#C205051)
+* insert child(#C204971,#C205014)
+* insert child(#C204971,#C204890)
+* insert child(#C204971,#C134254)
+* insert child(#C204971,#C134002)
+
+// Different value set that still requires hierarchies
+// Should this be its own supplement? 
+
+// * #C45299 "Gas"
+// * #C45298 "Liquid"
+* insert child(#C45298,#C154598) // "Liquid" -> "Solution"
+// * #C149895 "Semi-solid"
+// * #C45300 "Solid"
+* insert child(#C45300,#C154433) // "Solid" -> "Capsule"
+* insert child(#C45300,#C154605) // "Solid" -> "Tablet"
+
+