From f8129e888218a96a242b23ce78aefd8155e63ae8 Mon Sep 17 00:00:00 2001 From: SimonKonar Date: Mon, 14 Oct 2024 08:40:29 +0200 Subject: [PATCH 1/3] refactor descriptions --- MiabisOnFHIR/input/fsh/profiles/condition.fsh | 4 ++-- MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh | 6 +++--- MiabisOnFHIR/input/fsh/profiles/donor.fsh | 2 +- MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh | 2 +- MiabisOnFHIR/input/fsh/profiles/sample.fsh | 6 +++--- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/MiabisOnFHIR/input/fsh/profiles/condition.fsh b/MiabisOnFHIR/input/fsh/profiles/condition.fsh index 5d31d8c..926c585 100644 --- a/MiabisOnFHIR/input/fsh/profiles/condition.fsh +++ b/MiabisOnFHIR/input/fsh/profiles/condition.fsh @@ -16,8 +16,8 @@ Description: "This profile represents a condition, which is linked to sample and * code 0..1 MS * code ^short = "ICD-10 Code representing diagnosis of the patient." * code ^definition = "The ICD-10 code of the condition. This code is used to represent only the diagnosis of the patient. It is not used to represent the condition of the sample. For the condition of the sample, use the stage.assessment element." -* code from http://hl7.org/fhir/ValueSet/icd-10 +* code from DiagnosisVS * stage.assessment only Reference(DiagnosisReport) * stage.assessment 1.. MS * stage.assessment ^short = "Diagnostic Report" -* stage.assessment ^definition = "This element is used to link the condition to the sample and to the diagnosis of the said sample. It is used to represent the condition of the sample. For the diagnosis of the patient, use the code element." \ No newline at end of file +* stage.assessment ^definition = "This element is used to link the condition to the sample and to the diagnosis of the said sample. It is used to represent the condition of the sample. For the diagnosis of the patient (which is not linked to a specific sample, ie condition that patient has been diagnoses elsewhere), use the code element." \ No newline at end of file diff --git a/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh b/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh index d28a6a5..2e5a3a7 100644 --- a/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh +++ b/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh @@ -2,11 +2,11 @@ Profile: DiagnosisReport Parent: DiagnosticReport Id: miabis-diagnosis-report Title: "Diagnosis Report" -Description: "provides information about the diagnosis linked to sample" +Description: "Diagnosis Report provides information about the diagnosis linked to sample" * identifier 0..1 MS -* identifier ^short = "ID of Condition" -* identifier ^definition = "A unique identifier for the condition." +* identifier ^short = "ID of Diagnosis Report" +* identifier ^definition = "A unique identifier for the Diagnosis Report." * status = #final diff --git a/MiabisOnFHIR/input/fsh/profiles/donor.fsh b/MiabisOnFHIR/input/fsh/profiles/donor.fsh index cbd5246..dc725e8 100644 --- a/MiabisOnFHIR/input/fsh/profiles/donor.fsh +++ b/MiabisOnFHIR/input/fsh/profiles/donor.fsh @@ -18,5 +18,5 @@ Description: "Sample donor is a person who is a source of either a biological ma * birthDate ^definition = " Date of birth is required when Event date in Event resource is used, otherwise partial date, as in birth year, can be used" * extension contains DatasetTypeExtension named datasetType 0.. MS -* extension ^short = "Data categories" +* extension[datasetType] ^short = "Data categories" * extension[datasetType] ^definition = "The data categories from which data are available or can be linked to the sample donor. Can be several values" diff --git a/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh b/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh index 1f227c4..eb7c27c 100644 --- a/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh +++ b/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh @@ -14,7 +14,7 @@ Description: "Network Organization represent a formal part of a network member, * telecom ^short = "Complete http-address for the network." * telecom.system = #url * telecom.value 0..1 MS -* telecom.value ^short = "URL of the collection." +* telecom.value ^short = "URL of the network." * active 0..1 MS * active ^short = "The state of the network functions." * active ^definition = "The state of the network functions." diff --git a/MiabisOnFHIR/input/fsh/profiles/sample.fsh b/MiabisOnFHIR/input/fsh/profiles/sample.fsh index f9c9084..74b3f11 100644 --- a/MiabisOnFHIR/input/fsh/profiles/sample.fsh +++ b/MiabisOnFHIR/input/fsh/profiles/sample.fsh @@ -8,16 +8,16 @@ Description: "Sample is a portion or quantity of biological material that is col * identifier 1..1 MS * identifier ^short = "Sample ID" -* identifier ^definition = "Unique ID of the sample within a sample collection." +* identifier ^definition = "Unique ID of the sample usually given by the data provider." * collection.collectedDateTime ^short = "Sample creation date and time" -* collection.collectedDateTime ^definition = "The date and time the sample was created in the form previously described in detailedSampleType. Date/time format must be ISO8601-compliant or partial, for example, YYYY" +* collection.collectedDateTime ^definition = "The date and time the sample was created." * collection.collectedDateTime 0..1 MS * type from DetailedSampleTypeVS * type 1..1 MS * type ^short = "Detailed Sample type" -* type ^definition = "The type of biological specimen intended for testing diagnostics, disease propagation, treatment, or for research purposes." +* type ^definition = "The type of biological specimen." * collection.bodySite.coding obeys SpecimenOntologyInvariant * collection.bodySite.coding 0..1 MS From c3ee2aa76ea471410c5f463f385d1a4661bb9430 Mon Sep 17 00:00:00 2001 From: SimonKonar Date: Mon, 14 Oct 2024 08:51:03 +0200 Subject: [PATCH 2/3] refactor --- .../codeSystems/CollectionDatasetTypeCS.fsh | 2 +- ...biobankBioprocessingAndAnalyticasCapCS.fsh | 1 - .../biobankOrganisationalCapabilitiesCS.fsh | 2 +- .../fsh/codeSystems/collectionDesignCS.fsh | 1 - .../fsh/codeSystems/inclusionCriteriaCS.fsh | 2 +- .../input/fsh/codeSystems/materialTypeCS.fsh | 2 +- .../networkCommonCollaborationTopicCS.fsh | 2 +- .../codeSystems/sampleCollectionSettingCS.fsh | 2 +- .../input/fsh/profiles/collectionList.fsh | 19 ---------------- .../input/fsh/profiles/managingPerson.fsh | 22 ------------------- .../input/fsh/profiles/networkList.fsh | 18 --------------- .../input/fsh/valueSets/SampleSourceVS.fsh | 2 +- .../fsh/valueSets/collectionDatasetTypeVS.fsh | 2 +- .../input/fsh/valueSets/datasetTypeVS.fsh | 2 +- .../input/fsh/valueSets/materialTypeVS.fsh | 2 +- 15 files changed, 10 insertions(+), 71 deletions(-) delete mode 100644 MiabisOnFHIR/input/fsh/profiles/collectionList.fsh delete mode 100644 MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh delete mode 100644 MiabisOnFHIR/input/fsh/profiles/networkList.fsh diff --git a/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh index 2575147..ef9c200 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh @@ -2,7 +2,7 @@ CodeSystem: CollectionDatasetTypeCS Id: miabis-collection-dataset-typeCS Title: "MIABIS Collection Dataset Type" Description: "Codes describing the type of dataset that is part of a collection." -// create these : Lifestyle dataset, Environmental dataset, Physiological dataset, Biochemical dataset, Clinical dataset, Psychological dataset, Genomic dataset, Proteomic dataset, Metabolomic dataset, Body (Radiological) image, Whole slide image, Photo image, Genealogical records, Other. + * #Lifesyle "Lifestyle dataset" * #Environmental "Environmental dataset" * #Physiological "Physiological dataset" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh index 3d89322..dad0e3d 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh @@ -3,7 +3,6 @@ Id: miabis-bioprocessing-and-analytical-capabilities-cs Title: "Bioprocessing and Analytical Capabilities Code System" Description: "Code system representing the bioprocessing and analytical services that the biobank can offer to the clients. " -// Biochemical analyses, Genomics, Nucleic acid extraction, Proteomics, Metabolomics, Histology, Cell-lines processing, Virology, Sample processing, Sample shipping, Sample quality control services, Other * #BioChemAnalyses "Biochemical analyses" * #Genomics "Genomics" * #NucleicAcidExtraction "Nucleic acid extraction" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh index 62291f1..adb7e4f 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh @@ -2,7 +2,7 @@ CodeSystem: OrganisationalCapabilitiesCS Id: miabis-organisational-capabilities-cs Title: "Organisational Capabilities" Description: "This code system represents the organisational capabilities and services that the biobank can provide to support clients." -// Recontact with donors, Facilitating clinical trials, Setting up prospective collections, Access to omics data, Access to laboratory analysis data, Access to donors'clinical data, Access to pathology archive, Access to radiology archive, Access to national medical registries, Other + * #RecontactDonors "Recontact with donors" * #ClinicalTrials "Facilitating clinical trials" * #ProspectiveCollections "Setting up prospective collections" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh index ac7f7bc..491a143 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh @@ -3,7 +3,6 @@ Id: miabis-collection-design-cs Title: "MIABIS Collection Design code System" Description: "Codes describing the overall design of the collection that explains how the collection was/is built up." -// Case-control, Cross-sectional, Longitudinal cohort, Twin-study, Quality control study, Population-based cohort, Disease-specific cohort, Birth cohort, Microbial collection (if applicable with resistance data), Reference collection, Rare disease collection, Other. * #CaseControl "Case-control" * #CrossSectional "Cross-sectional" * #LongitudinalCohort "Longitudinal cohort" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh index 76e50de..2b082aa 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh @@ -2,7 +2,7 @@ CodeSystem: InclusionCriteriaCS Id: miabis-inclusion-criteria-cs Title: "Inclusion Criteria" Description: "Code system describing information on type of parameters that determine which subjects will become collection participant" -// Health status, Hospital patient, Use of medication, Gravidity, Age group, Familial status, Sex, Country of residence, Ethnic origin, Population representative sampling, Lifestyle/Exposure, Other + * #HealthStatus "Health status" * #HospitalPatient "Hospital patient" * #UseOfMedication "Use of medication" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh index 7b4c97b..1192a18 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh @@ -3,7 +3,7 @@ Id: miabis-material-type-CS Title: "MIABIS Material Type Code System" Description: "Codes for the material type of a sample" -// Codes are taken from https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#miabis-20-14 + * #Blood "Blood that has not been separated into its various components" * #DNA "DNA" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh index 3cd677f..224676a 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh @@ -3,7 +3,7 @@ Id: miabis-common-collaboration-topics-cs Title: "Common Collaboration Topics Code System" Description: "Codes describing topics that the network partners collaborate on" -// Common charter, Common SOPs, Common data access policy, Common sample access, policy, Common MTA, Common image access policy, Common image MTA, Common representation, Common URL, Other. + * #Charter "Common Charter" * #SOP "Common SOPs" * #DataAccessPolicy "Common data access policy" diff --git a/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh index 0a77724..b6e522e 100644 --- a/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh +++ b/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh @@ -3,7 +3,7 @@ Id: miabis-sample-collection-setting-cs Title: "MIABIS Sample Collection Setting Code System" Description: "Code set for the context in which the sample collection was conducted." -// Routine health care setting, Clinical trial, Research study, Public health/population based study, Museum and/or archeological collection, Environment, Unknown, Other. + * #RoutineHealthCare "Routine health care setting" * #ClinicalTrial "Clinical trial" * #ResearchStudy "Research study" diff --git a/MiabisOnFHIR/input/fsh/profiles/collectionList.fsh b/MiabisOnFHIR/input/fsh/profiles/collectionList.fsh deleted file mode 100644 index de93b7d..0000000 --- a/MiabisOnFHIR/input/fsh/profiles/collectionList.fsh +++ /dev/null @@ -1,19 +0,0 @@ -Profile: ListOfSpecimens -Parent: List -Id: miabis-list-of-specimens -Title: "List of specimens" -Description: "List of specimens belonging to a Collection resource" - -* mode = #working -* title 1..1 MS -* title ^short = "Name of collection this list belongs to" - -* subject only Reference(Collection) -* subject 1..1 MS -* subject ^short = "Collection this list belongs to" - -* entry 0..* MS -* entry.date 1..1 MS -* entry.item only Reference(Specimen) -* entry.item 1..1 MS -* entry.deleted 1..1 MS diff --git a/MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh b/MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh deleted file mode 100644 index d53fccc..0000000 --- a/MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh +++ /dev/null @@ -1,22 +0,0 @@ -Profile: ManagingPerson -Parent: Practitioner -Id: miabis-related-person -Title: "Managing Person" -Description: "Managing person of collection" - -* name 1..1 MS -* name ^short = "Name of the managing person" -* name.family 1..1 MS -* name ^short = "Family name of the managing person" -* name.given 1..1 MS -* name ^short = "Given name of the managing person" -* telecom 1..* MS -* address 1..1 MS -* address.line 1..* MS -* address.line ^short = "Street name and number" -* address.city 1..1 MS -* address.city ^short = "City of the managing person" -* address.postalCode 1..1 MS -* address.postalCode ^short = "Postal code of the managing person" -* address.country 1..1 MS -* address.country ^short = "Country of the managing person" \ No newline at end of file diff --git a/MiabisOnFHIR/input/fsh/profiles/networkList.fsh b/MiabisOnFHIR/input/fsh/profiles/networkList.fsh deleted file mode 100644 index 2f2ee19..0000000 --- a/MiabisOnFHIR/input/fsh/profiles/networkList.fsh +++ /dev/null @@ -1,18 +0,0 @@ -Profile: NetworkMembers -Parent: List -Id: miabis-network-members -Title: "Network Members" -Description: "This resource contains a list of all members of specified network." - -* mode = #working -* title 1..1 MS -* title ^short = "Name of collection this list belongs to" - -* subject only Reference(Network) -* subject 1..1 MS -* subject ^short = "Network this list belongs to" - -* entry 0..* MS -* entry.date 1..1 MS -* entry.item only Reference(Collection or Biobank) -* entry.item 1..1 MS \ No newline at end of file diff --git a/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh index 1a1f809..e66e92e 100644 --- a/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh +++ b/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh @@ -1,5 +1,5 @@ ValueSet: SampleSourceVS -Id: miabis-sample-source-VS +Id: miabis-sample-source-vs Title: "Sample Source Value Set" Description: "Value set containing the possible sources of a sample." diff --git a/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh index 5f76c7c..b571950 100644 --- a/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh +++ b/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh @@ -1,5 +1,5 @@ ValueSet: CollectionDatasetTypeVS -Id: miabis-collection-dataset-type +Id: miabis-collection-dataset-type-vs Title: "MIABIS Collection Dataset Type" Description: "Value set containing codes describing the type of dataset that is part of a collection." * include codes from system CollectionDatasetTypeCS \ No newline at end of file diff --git a/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh index eb0fa6d..8cfc56a 100644 --- a/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh +++ b/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh @@ -1,5 +1,5 @@ ValueSet: DatasetTypeVS -Id: miabis-dataset-type +Id: miabis-dataset-type-vs Title: "dataset type Value Set" Description: "The data categories from which data are available or can be linked to the sample donor. Can be one or more of the provided values" diff --git a/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh index 728a531..96c860b 100644 --- a/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh +++ b/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh @@ -1,5 +1,5 @@ ValueSet: MaterialTypeVS -Id: miabis-material-type-VS +Id: miabis-material-type-vs Title: "Material Type Value Set" Description: "Value set containing codes for the material type of the sample." From 018dd125a5c10bfe41f45c577dbde20ccb00da8a Mon Sep 17 00:00:00 2001 From: SimonKonar Date: Mon, 14 Oct 2024 09:05:42 +0200 Subject: [PATCH 3/3] refactor --- MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh b/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh index 915cdc6..acf6324 100644 --- a/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh +++ b/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh @@ -38,7 +38,7 @@ Description: "example of a collection instance" * extension[numberOfSubjects].valueInteger = 100 * extension[inclusionCriteria].valueCodeableConcept = InclusionCriteriaCS#HealthStatus - +* extension[MemberEntity].valueReference = Reference(Specimen/sampleId)