diff --git a/fsh.ini b/fsh.ini index 8898862a3..5693f744c 100644 --- a/fsh.ini +++ b/fsh.ini @@ -1,3 +1,3 @@ [FSH] -sushi-version = 3.6.0 +sushi-version = 3.11.0 timeout = 240 \ No newline at end of file diff --git a/input/fsh/EX_PhenotypicFeature.fsh b/input/fsh/EX_PhenotypicFeature.fsh deleted file mode 100644 index 3e4aec60e..000000000 --- a/input/fsh/EX_PhenotypicFeature.fsh +++ /dev/null @@ -1,48 +0,0 @@ -Instance: arachnodactyly -InstanceOf: PhenotypicFeature -Description: "PhenotypicFeature Example for arachnodactyly" -* status = #final "final" -* subject = Reference(example-patient) -* code = $hpo#HP:0001166 "Arachnodactyly" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - - -Instance: lvdysfunction-excluded -InstanceOf: PhenotypicFeature -Description: "PhenotypicFeature Example for exclusion of LV dysfunction" -* status = #final "final" -* subject = Reference(example-patient) -* code = $hpo#HP:0025168 "Left ventricular diastolic dysfunction" -* valueCodeableConcept = $LOINC#LA9634-2 "Absent" - -Instance: MVP-with-onset -InstanceOf: PhenotypicFeature -Description: "PhenotypicFeature Example for mitral value prolapse with onset" -* status = #final "final" -* subject = Reference(example-patient) -* code = $hpo#HP:0001634 "Mitral valve prolapse" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" -* effectiveDateTime = "2018-03-06" - -Instance: CHF-with-severity -InstanceOf: PhenotypicFeature -Description: "PhenotypicFeature Example for severe Low-output congestive heart failure" -* status = #final "final" -* subject = Reference(example-patient) -* code = $hpo#HP:0009805 "Low-output congestive heart failure" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" -* effectiveDateTime = "2018-03-06" -* component.code = $hpo#HP:0012824 "Severity" -* component.valueCodeableConcept = $hpo#HP:0012828 "Severe" - - -Instance: Polydactyly-with-modifier -InstanceOf: PhenotypicFeature -Description: "Bilateral postaxial Polydactyly, example to demonstrate use of Clinical Modifier" -* status = #final "final" -* subject = Reference(example-patient) -* code = $hpo#HP:0001162 "Postaxial hand polydactyly" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" -* effectiveDateTime = "2022-09-18" -* component.code = $hpo#HP:0012823 "Clinical modifier" -* component.valueCodeableConcept = $hpo#HP:0012832 "Bilateral" diff --git a/input/fsh/EX_RD_Phenopacket.fsh b/input/fsh/EX_RD_Phenopacket.fsh deleted file mode 100644 index 84c226027..000000000 --- a/input/fsh/EX_RD_Phenopacket.fsh +++ /dev/null @@ -1,191 +0,0 @@ -Instance: DevelopmentalDelay -InstanceOf: Phenopacket -Description: "Example use case for a child with undiagnosed developmental delay" -* identifier.value = "id.treatment.1" -* status = #preliminary "preliminary" -* type = $LOINC#11516-2 "Physician Episode of care medical records" -* date = "2018-03-16" -* title = "Phenopacket (static snapshot of clinical findings to support differential diagnosis of a child with developmental delay)." -* author = Reference(PeterGeneticist) -* subject = Reference(Proband1) -* section[phenotypic_features].entry[+] = Reference(longPhiltrum) -* section[phenotypic_features].entry[+] = Reference(microphthalmia) -* section[phenotypic_features].entry[+] = Reference(retinalDetachment) -* section[phenotypic_features].entry[+] = Reference(tga) -* section[phenotypic_features].entry[+] = Reference(reducedVisualAcuity) -* section[phenotypic_features].entry[+] = Reference(lowSetEars) -* section[phenotypic_features].entry[+] = Reference(globalDevelopmentalDelay) -* section[phenotypic_features].entry[+] = Reference(muscleWeakness) -* section[phenotypic_features].entry[+] = Reference(hypotonia) -* section[phenotypic_features].entry[+] = Reference(amyotrophy) -* section[phenotypic_features].entry[+] = Reference(fiberSizeVariability) -* section[biosamples].entry[+] = Reference(muscleBiopsy) -* section[diseases].entry[0] = Reference(intellectualDisabilityDisease) - - - -Instance: intellectualDisabilityDisease -InstanceOf: Disease -Description: "Intellectual disability (disease)" -* code = $mondo#MONDO_0001071 "Intellectual disability" -* subject = Reference(Proband1) - - -Instance: longPhiltrum -InstanceOf: PhenotypicFeature -Description: "Long philtrum (HP:0000343)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0000343 "Long philtrum" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: microphthalmia -InstanceOf: PhenotypicFeature -Description: "Long philtrum (HP:0000568)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0000568 "Microphthalmia" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: retinalDetachment -InstanceOf: PhenotypicFeature -Description: "Retinal detachment (HP:0000541)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0000541 "Retinal detachment" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: tga -InstanceOf: PhenotypicFeature -Description: "Transposition of the great arteries (HP:0001669)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0001669 "Transposition of the great arteries" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: reducedVisualAcuity -InstanceOf: PhenotypicFeature -Description: "Reduced visual acuity (HP:0007663)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0007663 "Reduced visual acuity" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: lowSetEars -InstanceOf: PhenotypicFeature -Description: "Low-set ears (HP:0000369)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0000369 "Reduced visual acuity" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: hypotonia -InstanceOf: PhenotypicFeature -Description: "Hypotonia (HP:0001252)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0001252 "Hypotonia" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - - -Instance: globalDevelopmentalDelay -InstanceOf: PhenotypicFeature -Description: "Global developmental delay (HP:0001263)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0001263 "Global developmental delay" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - -Instance: muscleWeakness -InstanceOf: PhenotypicFeature -Description: "Muscle weakness (HP:0001324)" -* status = #final "final" -* subject = Reference(Proband1) -* code = $hpo#HP:0001324 "Muscle weakness" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - - -Instance: amyotrophy -InstanceOf: PhenotypicFeature -Description: "Skeletal muscle atrophy (HP:0003202)" -* status = #final "Final" -* subject = Reference(Proband1) -* code = $hpo#HP:0003202 "Skeletal muscle atrophy" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - - - - - - -Instance: Proband1 -InstanceOf: Individual -Description: "Example child with developmental delay" -* identifier.use = #usual -* identifier.type = $IDTYPE#MR "Medical Record Number" -* identifier.system = "http://hospital.example.org" -* identifier.value = "m123" -* name.family = "Anyperson" -* name.given[0] = "Anyname" -* name.given[1] = "A." -* contact.telecom[0].system = #phone -* contact.telecom[0].value = "777-444-2222" -* contact.telecom[0].use = #home -* contact.telecom[1].system = #email -* contact.telecom[1].value = "anyname.anyperson@example.com" -* gender = #male -* birthDate = "2017-01-20" -* address.line = "123 Any St" -* address.city = "Anytown" -* address.postalCode = "12345" -* address.country = "US" -* communication.language = urn:ietf:bcp:47#en-US "English (Region=United States)" -* communication.language.text = "English" - - - -Instance: PeterGeneticist -InstanceOf: Practitioner -Description: "Extended example: example practitioner" -* identifier.value = "practitioner.id1" -* name.family = "Geneticist" -* name.given[0] = "Peter" -* name.prefix[0] = "Dr." -* address.use = #work -* address.line[0] = "123 Yellow Brick Drive" -* address.city = "Anytown" -* address.state = "MA" -* address.postalCode = "12345" -* address.country = "US" -* gender = #male -* qualification.code = http://terminology.hl7.org/CodeSystem/v2-0360#MD -* qualification.code.coding[0].version = "2.7" - - - -Instance: muscleBiopsy -InstanceOf: Biosample -Description: "Biosample Example -- muscle biopsy" -* id = "biosample.specimen.id.2" -* collection.bodySite = $uberon#UBERON_0001388 "gastrocnemius" -//* type = $efo#EFO_0010942 "primary tumor sample" -* subject = Reference(Proband1) -* identifier.value = "arbitrary identifier" -* extension[MaterialSample].valueCodeableConcept = $efo#EFO_0009655 "abnormal sample" -* processing.procedure = $ncit#NCIT_C51895 "Muscle Biopsy" -* collection.collectedDateTime = "2021-01-20" - - -Instance: fiberSizeVariability -InstanceOf: PhenotypicFeature -Description: "Increased variability in muscle fiber diameter (HP:0003557)" -* id = "hp.0003557" -* status = #final "Final" -* focus = Reference(muscleBiopsy) -* code = $hpo#HP:0003557 "Increased variability in muscle fiber diameter" -* valueCodeableConcept = $LOINC#LA9633-4 "Present" - - - - - diff --git a/input/fsh/Phenopackets-Genomics-Extensions.fsh b/input/fsh/Phenopackets-Genomics-Extensions.fsh deleted file mode 100644 index eac348f7f..000000000 --- a/input/fsh/Phenopackets-Genomics-Extensions.fsh +++ /dev/null @@ -1,105 +0,0 @@ -//Declaring an extension for xrefs -Extension: RelatedConceptID -Id: related-concept-id -Title: "Related Concept ID" -Description: "Used to provide identifiers to alternative resources representing related, but not equivalent concepts, for example gene ortholog ids" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only Identifier -//* valueIdentifier 0..1 //We may not need to declare this - -//Declaring an extension for additional identifier of the variant -Extension: AdditionalVariantIdentifier -Id: additional-variant-identifier -Title: "Additional Variant Identifier" -Description: "Used to list of unique identifiers where available. If this is a dbSNP variant, component[dbSNP-id] should be used instead." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only Identifier - -//Declaring an extension for Phred score of alternative alleles -Extension: PhredQualityScore -Id: phred-quality-score -Title: "Phred Quality Score" -Description: "Used to include Phred-scaled quality score for the assertion made in ALT." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only Quantity // Do you prefer another FHIR data type? // make it a floating point - -// Declaring an extension for the filter status -Extension: FilterStatus -Id: filter-status -Title: "Filter Status" -Description: "Filter status: PASS if this position has passed all filters." // More informative description may need to be added. -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only CodeableConcept or string - -Extension: VCFInfo -Id: vcf-info -Title: "VCF Info" -Description: "Additional information: Semicolon-separated series of additional information fields from VCF info field." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only string - -Extension: InterpretationStatus -Id: interpretation-status -Title: "Interpretation Status" -Description: "Describes the conclusion made about the genomic interpretation." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only CodeableConcept -* valueCodeableConcept 1..1 -* valueCodeableConcept from InterpretationStatusVS (required) -* . ^isModifier = true -* . ^isModifierReason = "The interpretation status could be REJECTED which may affect how the whole interpretation is interpreted." - -Extension: AcmgPathogenicityClassification -Id: acmg-pathogenicity-classification -Title: "ACMG Pathogenicity Classification" -Description: "One of the five ACMG pathogenicity categories, default is UNCERTAIN_SIGNIFICANCE." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only CodeableConcept -* valueCodeableConcept 1..1 -* valueCodeableConcept from AcmgPathogenicityClassificationVS (required) - -Extension: TherapeuticActionability -Id: therapeutic-actionability -Title: "Therapeutic Actionability" -Description: "one of the five ACMG pathogenicity categories, or NOT_PROVIDED. The default is NOT_PROVIDED." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only CodeableConcept -* valueCodeableConcept 1..1 -* valueCodeableConcept from TherapeuticActionabilityVS (required) - -Extension: VrsObject -Id: vrs-object -Title: "VRS Object" -Description: "The VRS Variation object (Link: https://vrs.ga4gh.org/en/stable/)" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only Attachment -* valueAttachment 1..1 - -Extension: MoleculeContext -Id: molecule-context -Title: "Molecule Context" -Description: "The molecular context of the vrs variation." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* value[x] only CodeableConcept -* valueCodeableConcept 1..1 -* valueCodeableConcept from MoleculeContextVS (required) \ No newline at end of file diff --git a/input/fsh/Phenopackets-Genomics-Instances.fsh b/input/fsh/Phenopackets-Genomics-Instances.fsh deleted file mode 100644 index 7f4878e63..000000000 --- a/input/fsh/Phenopackets-Genomics-Instances.fsh +++ /dev/null @@ -1,82 +0,0 @@ -Instance: PhenopacketsVariantExample01 -InstanceOf: PhenopacketsVariant // we may use the URL later to refer to this profile -Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors -Title: "Phenopackets Variant Example-1" -Description: "This is an example of phenopackets-genomic-interpretation - which is a phenopackets profile of the genomics reporting Variant profile. - It represents phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, - and VariantInterpretation building blocks." -* status = #final - -Instance: PhenopacketsGenomicInterpretationExample01 -InstanceOf: PhenopacketsGenomicInterpretation // we may use the URL later to refer to this profile -Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors -Title: "Phenopackets Genomic Interpretation Example-1" -Description: "This is an example of phenopackets-variant which is a phenopackets profile of - the genomics reporting Genomics Report profile. - It represents phenopackets GenomicInterpretation building block, i.e., the - interpretation for an individual variant or gene." -* specimen = Reference(phenopacketSpecimenExample01) // we may need to use a real specimen example -* subject = Reference(phenopacketPatientExample01) -* category[Genetics] = http://terminology.hl7.org/CodeSystem/v2-0074#GE "Genetics" -* modifierExtension[interpretationStatus].valueCodeableConcept = PPIS#0 "UNKNOWN_STATUS" -* result[variant] = Reference(PhenopacketsVariantExample01) -* conclusion = "The detected variant is Likely-Pathogenic of Pfeiffer syndrome" -* conclusionCode.coding = $sct#70410008 "Acrocephalosyndactyly type V (disorder)" -* code = http://loinc#123 "some loinc code" - -Instance: PhenopacketsGenomicInterpretationExample02 -InstanceOf: PhenopacketsGenomicInterpretation // we may use the URL later to refer to this profile -Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors -Title: "Phenopackets Genomic Interpretation Example-2" -Description: "This is an example of phenopackets-variant which is a phenopackets profile of - the genomics reporting Genomics Report profile. - It represents phenopackets GenomicInterpretation building block, i.e., the - interpretation for an individual variant or gene." -* identifier.value = "02" -* specimen = Reference(phenopacketSpecimenExample01) // we may need to use a real specimen example -* subject = Reference(phenopacketPatientExample01) -* category[Genetics] = http://terminology.hl7.org/CodeSystem/v2-0074#GE "Genetics" -* modifierExtension[interpretationStatus].valueCodeableConcept = PPIS#0 "UNKNOWN_STATUS" -* result[variant] = Reference(PhenopacketsVariantExample01) -* conclusion = "A rare genetic form of obesity characterized by morbid obesity, hypertension, type 2 diabetes mellitus and dyslipidemia leading to early coronary disease, myocardial infarction and congestive heart failure. Intellectual disability and decreased sperm counts or azoospermia have also been reported." -* conclusionCode.coding = $sct#783549006 "Obesity due to centrosomal protein 19 deficiency (disorder)" -* code = http://loinc#123 "some loinc code" - -Instance: phenopacketSpecimenExample01 -InstanceOf: Specimen -Usage: #example -Title: "phenopacket Specimen Example01" -Description: "This is an incomplete example that used as - a placeholder for a curated specimen example" -* identifier.value = "01" -* identifier.use = #temp -* text.status = #generated -* text.div = "
This is an incomplete example that used as - a placeholder for a curated specimen example
" -* subject = Reference(phenopacketPatientExample01) - -Instance: phenopacketPatientExample01 -InstanceOf: Patient -Usage: #example -Title: "phenopacket Patient Example01" -Description: "This is an example of a patient resource to be used in the assocaited patient examples. It is not representative of phenopackets patient's data representation" -* identifier.value = "04" -* identifier.use = #temp -* name.given = "John" -* name.family = "Doe" -* gender = #unknown - - -Instance: PhenopacketPractitionerExample01 -InstanceOf: Practitioner -Usage: #example -Title: "phenopacket Practitioner Example01" -Description: "This is an incomplete example that used as - a placeholder for a curated Practitioner example" -* identifier.value = "03" -* identifier.use = #temp -* text.status = #generated -* text.div = "
This is an incomplete example that used as - a placeholder for a curated Practitioner example
" -* name.text = "John T. Practitioner" diff --git a/input/fsh/Phenopackets-Genomics-Invariants.fsh b/input/fsh/Phenopackets-Genomics-Invariants.fsh deleted file mode 100644 index 78df677ab..000000000 --- a/input/fsh/Phenopackets-Genomics-Invariants.fsh +++ /dev/null @@ -1,51 +0,0 @@ -Invariant: phenopackets-subject-or-specimen-id // we may change the name of this invariant to be numbered. It was just kept to clearly reflect its purpose. -Description: "subject.id and/or specimen.id SHALL be present" -//Expression: "subject[Patient].identifier.exists() or specimen[Specimen].identifier.exists()" // we may need to revise this in corresponding patient and biosample mappings -Severity: #error -//XPath: ""//this is optional - -//Place-holder for an invariant that links variation components and molecule context extension -Invariant: phenopackets-moleculeContext-align-with-result-component -Description: "The extension[moleculeContext].value SHALL be aligned to the Variant results components for values - other than PPMC#0 'unspecified_molecule_context'. Where - - PPMC#1 'genomic' corresponds to variation-code; dna-chg; or genomic-dna-chg, - - PPMC#2 'transcript' corresponds to variation-code; or dna-chg; - - PPMC#3 'protein' corresponds to variation-code; or amino-acid-chg" -//Expression: "" -Severity: #error -//XPath: "" - -Invariant: phenopackets-one-variation-identifier-component -Description: "Only one of the following components SHALL be used to describe the intended variation - - component:variation-code - - component:dna-chg - - component:genomic-dna-chg.valueCodeableConcept - - component:amino-acid-chg.valueCodeableConcept" -//Expression: "" -Severity: #error -//XPath: "" - - - -//Place-holder for dbSNP-id variation identifier vs other CURIE identifiers invariant -Invariant: phenopackets-dbsnp-id-and-other-ids -Description: "component-dbSNP-id SHAll be used to represent dbSNP-ids. For other ids, corresponding components - SHALL be used" -//Expression: "" -Severity: #error -//XPath: "" - -//Place-holder for primary identifier and alternate identifiers invariant -/* This invariant is to be used with: - - VariationDescriptor.label+description and VariationDescriptor.alternateLabels - - GeneDescriptor.value_id+symbol and GeneDescriptor.alternate_symbols -*/ -Invariant: phenopackets-primary-and-alternate-ids-or-labels -Description: "primary ID SHALL be present in this component, while alternate id/lables and their associated ids/lables - SHALL be added to it, if present. They SHALL be add as additional codings within the valueCodeableConcept - of this element/component" -//Expression: "" -Severity: #warning //Is it better to be #error? -//XPath: "" - - diff --git a/input/fsh/Phenopackets-Genomics-ValueSets.fsh b/input/fsh/Phenopackets-Genomics-ValueSets.fsh deleted file mode 100644 index f43a7f1a6..000000000 --- a/input/fsh/Phenopackets-Genomics-ValueSets.fsh +++ /dev/null @@ -1,95 +0,0 @@ -/*This FSH file cotains the FHIR representations of phenopackets controlled terminologies/codes of genomics building blocks value sets */ -Alias: PPIS = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus -Alias: PPTA = http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#therapeuticactionability -Alias: PPAPC = http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#acmgpathogenicityclassification -Alias: PPMC = http://phenopacket-schema.readthedocs.io/en/v2/variant.html#rstmoleculecontext -Alias: SO = http://www.sequenceontology.org/ -Alias: GENO = http://www.ebi.ac.uk/ols/ontologies/geno -Alias: LNC = http://loinc.org -Alias: HGNC = http://www.genenames.org/ -Alias: HGVS = http://www.hgvs.org/ -Alias: dbSNP = http://www.ncbi.nlm.nih.gov/snp/ - -ValueSet: InterpretationStatusVS -Id: interpretationStatus-vs -Title: "Interpretation Status Value Set" -Description: "Describes the conclusion made about the genomic interpretation." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" -* PPIS#0 "UNKNOWN_STATUS" -* PPIS#1 "REJECTED" -* PPIS#2 "CANDIDATE" -* PPIS#3 "CONTRIBUTORY" -* PPIS#4 "CAUSATIVE" - -ValueSet: TherapeuticActionabilityVS -Id: therapeuticActionability-vs -Title: "Therapeutic Actionability Value Set" -Description: "Describes the therapeutic actionability of the variant." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" -* PPTA#0 "UNKNOWN_ACTIONABILITY" -* PPTA#1 "NOT_ACTIONABLE" -* PPTA#2 "ACTIONABLE" - -ValueSet: AcmgPathogenicityClassificationVS -Id: acmgPathogenicityClassification-vs -Title: "ACMG Pathogenicity Classification Value Set" -Description: "Describes the ACMG five-tier pathogenicity classification system (Richards et al., 2015, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/)." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" -* PPAPC#0 "NOT_PROVIDED" -* PPAPC#1 "BENIGN" -* PPAPC#2 "LIKELY_BENIGN" -* PPAPC#3 "UNCERTAIN_SIGNIFICANCE" -* PPAPC#4 "LIKELY_PATHOGENIC" -* PPAPC#5 "PATHOGENIC" - -ValueSet: MoleculeContextVS -Id: moleculeContext-vs -Title: "Molecule Context Value Set" -Description: "Describes The molecular context of the variant. Default is unspecified_molecule_context." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" -* PPMC#0 "unspecified_molecule_context" -* PPMC#1 "genomic" -* PPMC#2 "transcript" -* PPMC#3 "protein" - -ValueSet: SequenceOntologyStructuralVariantVS -Id: sequence-ontology-structural-variant-vs -Title: "Sequence Ontology Structural Variant Value Set" -Description: "Descendent terms of SO:0001537." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* include codes from system SO where concept is-a SO#SO:0001537 - -ValueSet: GenoOntologyAllelicStateVS -Id: geno-ontology-allelic-state-vs -Title: "GENO Ontology Allelic State Value Set" -Description: "Descendent terms of GENO_0000875" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* include codes from system GENO where concept is-a GENO#GENO_0000875 diff --git a/input/fsh/aliases.fsh b/input/fsh/aliases.fsh index 23cac291f..8d73db426 100644 --- a/input/fsh/aliases.fsh +++ b/input/fsh/aliases.fsh @@ -19,3 +19,14 @@ Alias: $umls = http://www.nlm.nih.gov/research/umls Alias: $units = http://purl.obolibrary.org/obo/uo.owl Alias: USCorePractitioner = http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner +/*This FSH file cotains the FHIR representations of phenopackets controlled terminologies/codes of genomics building blocks value sets */ +Alias: PPIS = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus +Alias: PPTA = http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#therapeuticactionability +Alias: PPAPC = http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#acmgpathogenicityclassification +Alias: PPMC = http://phenopacket-schema.readthedocs.io/en/v2/variant.html#rstmoleculecontext +Alias: SO = http://www.sequenceontology.org/ +Alias: GENO = http://www.ebi.ac.uk/ols/ontologies/geno +Alias: LNC = http://loinc.org +Alias: HGNC = http://www.genenames.org/ +Alias: HGVS = http://www.hgvs.org/ +Alias: dbSNP = http://www.ncbi.nlm.nih.gov/snp/ \ No newline at end of file diff --git a/input/fsh/codeSystems.fsh b/input/fsh/codeSystems.fsh deleted file mode 100644 index 6340aec6f..000000000 --- a/input/fsh/codeSystems.fsh +++ /dev/null @@ -1,89 +0,0 @@ -CodeSystem: Categories -Id: categories -Title: "Categories" -Description: "Various categories or tags" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableCodeSystem -* ^experimental = false -* ^caseSensitive = true -* ^content = #complete -* #phenotype "Phenotype" - - -CodeSystem: PhenotypicFeatureStatusCS -Id: phenotypicFeatureStatusCS -Title: "Categories" -Description: "Various categories or tags" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableCodeSystem -* ^experimental = false -* ^caseSensitive = true -* ^content = #complete -* #Absent "Absent" -* #Present "Present" - -CodeSystem: HtsFormat -Id: HtsFormat -Title: "HTS Format" -Description: "An enumeration used to represent different high-throughput sequencing file formats." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableCodeSystem -* ^experimental = false -* ^caseSensitive = true -* ^date = "2020-02-14T16:13:10+10:00" -* ^content = #complete -* #UNKNOWN "Unknown" -* #SAM "SAM" -* #BAM "BAM" -* #CRAM "CRAM" -* #VCF "VCF" -* #BCF "BCF" -* #GVCF "GVCF" - -CodeSystem: KaryotypicSexCS -Id: KaryotypicSex -Title: "Karyotypic sex code system" -Description: "karyotypic sex of an individual (also known as chromosomal sex)" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableCodeSystem -* ^experimental = false -* ^caseSensitive = true -* ^date = "2021-05-28T17:06:00-04:00" -* ^content = #complete -* #UNKNOWN_KARYOTYPE "UNKNOWN_KARYOTYPE" "Untyped or inconclusive karyotyping" -* #XX "XX karyotypic sex" "Karyotype with two X chromosomes" -* #XY "XY karyotypic sex" "Karyotype with one X chromosome and one Y chromosome" -* #XO "XO karyotypic sex" "Karyotype with one X chromosome" -* #XXY "XXY karyotypic sex" "Karyotype with two X chromosomes and one Y chromosome" -* #XXX "XXX karyotypic sex" "Karyotype with three X chromosomes" -* #XXYY "XXYY karyotypic sex" "Karyotype with two X chromosomes and two Y chromosomes" -* #XXXY "XXXY karyotypic sex" "Karyotype with three X chromosomes and one Y chromosome" -* #XXXX "XXXX karyotypic sex" "Karyotype with four X chromosomes" -* #XYY "XYY karyotypic sex" "Karyotype with one X chromosome and two Y chromosomes" -* #OTHER_KARYOTYPE "Other karyotype" "Karyotype with sex chromosomes other than XX,XY,X0,XXY,XXX,XXYY,XXXY,XXXX, or XYY" - -CodeSystem: SectionType -Id: section-type -Title: "Section Type" -Description: "Section Type" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableCodeSystem -* ^experimental = false -* ^caseSensitive = true -* #phenotypic_features -* #measurements -* #biosamples -* #interpretations -* #diseases -* #files -* #medicalActions diff --git a/input/fsh/codesystems/HtsFormat.fsh b/input/fsh/codesystems/HtsFormat.fsh new file mode 100644 index 000000000..94e08c9e5 --- /dev/null +++ b/input/fsh/codesystems/HtsFormat.fsh @@ -0,0 +1,19 @@ +CodeSystem: HtsFormat +Id: HtsFormat +Title: "HTS Format" +Description: "An enumeration used to represent different high-throughput sequencing file formats." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableCodeSystem +* ^experimental = false +* ^caseSensitive = true +* ^date = "2020-02-14T16:13:10+10:00" +* ^content = #complete +* #UNKNOWN "Unknown" +* #SAM "SAM" +* #BAM "BAM" +* #CRAM "CRAM" +* #VCF "VCF" +* #BCF "BCF" +* #GVCF "GVCF" diff --git a/input/fsh/codesystems/KaryotypicSex.fsh b/input/fsh/codesystems/KaryotypicSex.fsh new file mode 100644 index 000000000..0657aaa14 --- /dev/null +++ b/input/fsh/codesystems/KaryotypicSex.fsh @@ -0,0 +1,23 @@ +CodeSystem: KaryotypicSexCS +Id: KaryotypicSex +Title: "Karyotypic sex code system" +Description: "karyotypic sex of an individual (also known as chromosomal sex)" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableCodeSystem +* ^experimental = false +* ^caseSensitive = true +* ^date = "2021-05-28T17:06:00-04:00" +* ^content = #complete +* #UNKNOWN_KARYOTYPE "UNKNOWN_KARYOTYPE" "Untyped or inconclusive karyotyping" +* #XX "XX karyotypic sex" "Karyotype with two X chromosomes" +* #XY "XY karyotypic sex" "Karyotype with one X chromosome and one Y chromosome" +* #XO "XO karyotypic sex" "Karyotype with one X chromosome" +* #XXY "XXY karyotypic sex" "Karyotype with two X chromosomes and one Y chromosome" +* #XXX "XXX karyotypic sex" "Karyotype with three X chromosomes" +* #XXYY "XXYY karyotypic sex" "Karyotype with two X chromosomes and two Y chromosomes" +* #XXXY "XXXY karyotypic sex" "Karyotype with three X chromosomes and one Y chromosome" +* #XXXX "XXXX karyotypic sex" "Karyotype with four X chromosomes" +* #XYY "XYY karyotypic sex" "Karyotype with one X chromosome and two Y chromosomes" +* #OTHER_KARYOTYPE "Other karyotype" "Karyotype with sex chromosomes other than XX,XY,X0,XXY,XXX,XXYY,XXXY,XXXX, or XYY" diff --git a/input/fsh/codesystems/categories.fsh b/input/fsh/codesystems/categories.fsh new file mode 100644 index 000000000..126f53090 --- /dev/null +++ b/input/fsh/codesystems/categories.fsh @@ -0,0 +1,12 @@ +CodeSystem: Categories +Id: categories +Title: "Categories" +Description: "Various categories or tags" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableCodeSystem +* ^experimental = false +* ^caseSensitive = true +* ^content = #complete +* #phenotype "Phenotype" diff --git a/input/fsh/codesystems/phenotypicFeatureStatusCS.fsh b/input/fsh/codesystems/phenotypicFeatureStatusCS.fsh new file mode 100644 index 000000000..2b16c0095 --- /dev/null +++ b/input/fsh/codesystems/phenotypicFeatureStatusCS.fsh @@ -0,0 +1,13 @@ +CodeSystem: PhenotypicFeatureStatusCS +Id: phenotypicFeatureStatusCS +Title: "Categories" +Description: "Various categories or tags" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableCodeSystem +* ^experimental = false +* ^caseSensitive = true +* ^content = #complete +* #Absent "Absent" +* #Present "Present" diff --git a/input/fsh/codesystems/section-type.fsh b/input/fsh/codesystems/section-type.fsh new file mode 100644 index 000000000..b46324801 --- /dev/null +++ b/input/fsh/codesystems/section-type.fsh @@ -0,0 +1,17 @@ +CodeSystem: SectionType +Id: section-type +Title: "Section Type" +Description: "Section Type" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableCodeSystem +* ^experimental = false +* ^caseSensitive = true +* #phenotypic_features +* #measurements +* #biosamples +* #interpretations +* #diseases +* #files +* #medicalActions diff --git a/input/fsh/examples/1.fsh b/input/fsh/examples/1.fsh new file mode 100644 index 000000000..e69de29bb diff --git a/input/fsh/examples/6.fsh b/input/fsh/examples/6.fsh new file mode 100644 index 000000000..e69de29bb diff --git a/input/fsh/examples/7.fsh b/input/fsh/examples/7.fsh new file mode 100644 index 000000000..e69de29bb diff --git a/input/fsh/EX_Biosample.fsh b/input/fsh/examples/Biosample_bladderCarcinoma.fsh similarity index 100% rename from input/fsh/EX_Biosample.fsh rename to input/fsh/examples/Biosample_bladderCarcinoma.fsh diff --git a/input/fsh/examples/Biosample_muscleBiopsy.fsh b/input/fsh/examples/Biosample_muscleBiopsy.fsh new file mode 100644 index 000000000..ec97f4570 --- /dev/null +++ b/input/fsh/examples/Biosample_muscleBiopsy.fsh @@ -0,0 +1,11 @@ +Instance: muscleBiopsy +InstanceOf: Biosample +Description: "Biosample Example -- muscle biopsy" +* id = "biosample.specimen.id.2" +* collection.bodySite = $uberon#UBERON_0001388 "gastrocnemius" +//* type = $efo#EFO_0010942 "primary tumor sample" +* subject = Reference(Proband1) +* identifier.value = "arbitrary identifier" +* extension[MaterialSample].valueCodeableConcept = $efo#EFO_0009655 "abnormal sample" +* processing.procedure = $ncit#NCIT_C51895 "Muscle Biopsy" +* collection.collectedDateTime = "2021-01-20" diff --git a/input/fsh/Phenopackets_bundle_instances.fsh b/input/fsh/examples/Bundle_PhenopacketCompositionExample01.fsh similarity index 50% rename from input/fsh/Phenopackets_bundle_instances.fsh rename to input/fsh/examples/Bundle_PhenopacketCompositionExample01.fsh index 2b2447975..faba83fe3 100644 --- a/input/fsh/Phenopackets_bundle_instances.fsh +++ b/input/fsh/examples/Bundle_PhenopacketCompositionExample01.fsh @@ -1,37 +1,3 @@ -Instance: PhenopacketsBundleExample01 -InstanceOf: Bundle -Description: "Example Phenopacket Bundle instance" -Usage: #example -* meta.lastUpdated = "2022-02-02T22:22:22Z" -* identifier.system = "urn:ietf:rfc:3986" -* identifier.value = "urn:uuid:1111-1111-1111-1111" -* type = #document -* timestamp = "2022-02-02T22:22:22Z" -* entry[0] - * insert bundleEntry(Composition, PhenopacketCompositionExample01) -* entry[+] - * insert bundleEntry(Patient, example-patient) -* entry[+] - * insert bundleEntry(Practitioner, PhenopacketPractitionerExample01) -//features: CHF-with-severity -* entry[+] - * insert bundleEntry(Observation, CHF-with-severity) -//measurements: thrombocytopenia -* entry[+] - * insert bundleEntry(Observation, thrombocytopenia) -//diseases: CHF-stageIII -* entry[+] - * insert bundleEntry(Condition, CHF-stageIII) -//biosamples: bladderCarcinoma -* entry[+] - * insert bundleEntry(Specimen, bladderCarcinoma) -//interpretation: PhenopacketsGenomicInterpretationExample02 -* entry[+] - * insert bundleEntry(DiagnosticReport, PhenopacketsGenomicInterpretationExample02) -//PhenopacketsVariantExample01 -* entry[+] - * insert bundleEntry(Observation, PhenopacketsVariantExample01) - Instance: PhenopacketCompositionExample01 InstanceOf: Phenopacket Description: "Example Phenopacket Composition instance" diff --git a/input/fsh/examples/Bundle_PhenopacketsBundleExample01.fsh b/input/fsh/examples/Bundle_PhenopacketsBundleExample01.fsh new file mode 100644 index 000000000..c17867513 --- /dev/null +++ b/input/fsh/examples/Bundle_PhenopacketsBundleExample01.fsh @@ -0,0 +1,33 @@ +Instance: PhenopacketsBundleExample01 +InstanceOf: Bundle +Description: "Example Phenopacket Bundle instance" +Usage: #example +* meta.lastUpdated = "2022-02-02T22:22:22Z" +* identifier.system = "urn:ietf:rfc:3986" +* identifier.value = "urn:uuid:1111-1111-1111-1111" +* type = #document +* timestamp = "2022-02-02T22:22:22Z" +* entry[0] + * insert bundleEntry(Composition, PhenopacketCompositionExample01) +* entry[+] + * insert bundleEntry(Patient, example-patient) +* entry[+] + * insert bundleEntry(Practitioner, PhenopacketPractitionerExample01) +//features: CHF-with-severity +* entry[+] + * insert bundleEntry(Observation, CHF-with-severity) +//measurements: thrombocytopenia +* entry[+] + * insert bundleEntry(Observation, thrombocytopenia) +//diseases: CHF-stageIII +* entry[+] + * insert bundleEntry(Condition, CHF-stageIII) +//biosamples: bladderCarcinoma +* entry[+] + * insert bundleEntry(Specimen, bladderCarcinoma) +//interpretation: PhenopacketsGenomicInterpretationExample02 +* entry[+] + * insert bundleEntry(DiagnosticReport, PhenopacketsGenomicInterpretationExample02) +//PhenopacketsVariantExample01 +* entry[+] + * insert bundleEntry(Observation, PhenopacketsVariantExample01) diff --git a/input/fsh/EX_Disease.fsh b/input/fsh/examples/Disease_excluded-disease.fsh similarity index 100% rename from input/fsh/EX_Disease.fsh rename to input/fsh/examples/Disease_excluded-disease.fsh diff --git a/input/fsh/examples/Disease_intellectualDisabilityDisease.fsh b/input/fsh/examples/Disease_intellectualDisabilityDisease.fsh new file mode 100644 index 000000000..133a78f27 --- /dev/null +++ b/input/fsh/examples/Disease_intellectualDisabilityDisease.fsh @@ -0,0 +1,5 @@ +Instance: intellectualDisabilityDisease +InstanceOf: Disease +Description: "Intellectual disability (disease)" +* code = $mondo#MONDO_0001071 "Intellectual disability" +* subject = Reference(Proband1) diff --git a/input/fsh/examples/Individual_Proband1.fsh b/input/fsh/examples/Individual_Proband1.fsh new file mode 100644 index 000000000..79348ceac --- /dev/null +++ b/input/fsh/examples/Individual_Proband1.fsh @@ -0,0 +1,23 @@ +Instance: Proband1 +InstanceOf: Individual +Description: "Example child with developmental delay" +* identifier.use = #usual +* identifier.type = $IDTYPE#MR "Medical Record Number" +* identifier.system = "http://hospital.example.org" +* identifier.value = "m123" +* name.family = "Anyperson" +* name.given[0] = "Anyname" +* name.given[1] = "A." +* contact.telecom[0].system = #phone +* contact.telecom[0].value = "777-444-2222" +* contact.telecom[0].use = #home +* contact.telecom[1].system = #email +* contact.telecom[1].value = "anyname.anyperson@example.com" +* gender = #male +* birthDate = "2017-01-20" +* address.line = "123 Any St" +* address.city = "Anytown" +* address.postalCode = "12345" +* address.country = "US" +* communication.language = urn:ietf:bcp:47#en-US "English (Region=United States)" +* communication.language.text = "English" diff --git a/input/fsh/Ex_Individual.fsh b/input/fsh/examples/Individual_example-patient.fsh similarity index 100% rename from input/fsh/Ex_Individual.fsh rename to input/fsh/examples/Individual_example-patient.fsh diff --git a/input/fsh/EX_Measurement.fsh b/input/fsh/examples/Measurement_thrombocytopenia.fsh similarity index 100% rename from input/fsh/EX_Measurement.fsh rename to input/fsh/examples/Measurement_thrombocytopenia.fsh diff --git a/input/fsh/examples/Observation_karyotypic-sex-invalid-1.fsh b/input/fsh/examples/Observation_karyotypic-sex-invalid-1.fsh new file mode 100644 index 000000000..4e41c1ec8 --- /dev/null +++ b/input/fsh/examples/Observation_karyotypic-sex-invalid-1.fsh @@ -0,0 +1,8 @@ +Instance: karyotypic-sex-invalid-1 +InstanceOf: Observation +Title: "An INVALID karyotypic sex Observation instance." +Description: "An INVALID karyotypic sex Observation instance." +Usage: #example +* status = #final +* code = $GSSO#GSSO:000113 +* valueCodeableConcept = $observation-karyotypic-sex#XXW diff --git a/input/fsh/examples/Observation_karyotypic-sex-valid-1.fsh b/input/fsh/examples/Observation_karyotypic-sex-valid-1.fsh new file mode 100644 index 000000000..d1b3aa635 --- /dev/null +++ b/input/fsh/examples/Observation_karyotypic-sex-valid-1.fsh @@ -0,0 +1,8 @@ +Instance: karyotypic-sex-valid-1 +InstanceOf: Observation +Title: "A VALID karyotypic sex Observation instance." +Description: "A VALID karyotypic sex Observation instance." +Usage: #example +* status = #final +* code = $GSSO#GSSO:000113 +* valueCodeableConcept = $observation-karyotypic-sex#XX diff --git a/input/fsh/examples/Observation_phenotypic-abnormality-invalid-1.fsh b/input/fsh/examples/Observation_phenotypic-abnormality-invalid-1.fsh new file mode 100644 index 000000000..3209a9494 --- /dev/null +++ b/input/fsh/examples/Observation_phenotypic-abnormality-invalid-1.fsh @@ -0,0 +1,27 @@ +Instance: phenotypic-abnormality-invalid-1 +InstanceOf: Observation +Title: "An INVALID phenotypic abnormality Observation example." +Description: "An INVALID phenotypic abnormality Observation example." +Usage: #example +//* extension.url = "http://github.com/phenopackets/core-ig/ig-tools/validation-error-count" +//* extension.valueInteger = 4 +* status = #final +* code = $hpo#HP:0001249 "Intellectual disability" +* code.text = "Intellectual disability" +* valueBoolean = true +* component[0].code = $hpo#HP:0012824 "Severity" +* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" +* component[+].code = $hpo#HP:0012824 "Severity" +* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" +* component[+].code = $hpo#HP:0012823 "Clinical modifier" +* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" +* component[+].code = $hpo#HP:0012823 "Clinical modifier" +* component[=].valueCodeableConcept = $hpo#HP:0031375 "Refractory" +* component[+].code = $hpo#HP:0012823 "Clinical modifier" +* component[=].valueCodeableConcept = $hpo#HP:999999999 "Non existant modifier" +* component[+].code = $hpo#HP:0003674 "Onset" +* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" +* component[+].code = $hpo#HP:0003674 "Onset" +* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" +* component[+].code = $OTHER#OTHER "Severity" +* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" diff --git a/input/fsh/examples/Observation_phenotypic-abnormality-invalid-meta-profile.fsh b/input/fsh/examples/Observation_phenotypic-abnormality-invalid-meta-profile.fsh new file mode 100644 index 000000000..f270c862d --- /dev/null +++ b/input/fsh/examples/Observation_phenotypic-abnormality-invalid-meta-profile.fsh @@ -0,0 +1,23 @@ +//Instance: phenotypic-abnormality-invalid-meta-profile +//InstanceOf: Observation +//Usage: #example +//* status = #final +//* code = $hpo#HP:0001249 "Intellectual disability" +//* code.text = "Intellectual disability" +//* valueBoolean = true +//* component[0].code = $hpo#HP:0012824 "Severity" +//* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" +//* component[+].code = $hpo#HP:0012824 "Severity" +//* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" +//* component[+].code = $hpo#HP:0012823 "Clinical modifier" +//* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" +//* component[+].code = $hpo#HP:0012823 "Clinical modifier" +//* component[=].valueCodeableConcept = $hpo#HP:0031375 "Refractory" +//* component[+].code = $hpo#HP:0012823 "Clinical modifier" +//* component[=].valueCodeableConcept = $hpo#HP:999999999 "Non existant modifier" +//* component[+].code = $hpo#HP:0003674 "Onset" +//* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" +//* component[+].code = $hpo#HP:0003674 "Onset" +//* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" +//* component[+].code = $OTHER#OTHER "Severity" +//* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" \ No newline at end of file diff --git a/input/fsh/examples/Observation_phenotypic-abnormality-valid-1.fsh b/input/fsh/examples/Observation_phenotypic-abnormality-valid-1.fsh new file mode 100644 index 000000000..de390d45a --- /dev/null +++ b/input/fsh/examples/Observation_phenotypic-abnormality-valid-1.fsh @@ -0,0 +1,19 @@ +Instance: phenotypic-abnormality-valid-1 +InstanceOf: Observation +Title: "A valid phenotypic abnormality Observation example." +Description: "A valid phenotypic abnormality Observation example." +Usage: #example +* status = #final +* code = $hpo#HP:0001249 "Intellectual disability" +* code.text = "Intellectual disability" +* valueBoolean = true +* component[0].code = $hpo#HP:0012824 "Severity" +* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" +* component[+].code = $hpo#HP:0012823 "Clinical modifier" +* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" +* component[+].code = $hpo#HP:0003674 "Onset" +* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" +* component[+].code = $hpo#HP:0003674 "Onset" +* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" +* component[+].code = $OTHER#OTHER "Severity" +* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" diff --git a/input/fsh/examples/Patient_phenopacketPatientExample01.fsh b/input/fsh/examples/Patient_phenopacketPatientExample01.fsh new file mode 100644 index 000000000..3b42dcacb --- /dev/null +++ b/input/fsh/examples/Patient_phenopacketPatientExample01.fsh @@ -0,0 +1,10 @@ +Instance: phenopacketPatientExample01 +InstanceOf: Patient +Usage: #example +Title: "phenopacket Patient Example01" +Description: "This is an example of a patient resource to be used in the assocaited patient examples. It is not representative of phenopackets patient's data representation" +* identifier.value = "04" +* identifier.use = #temp +* name.given = "John" +* name.family = "Doe" +* gender = #unknown diff --git a/input/fsh/examples/Phenopacket_DevelopmentalDelay.fsh b/input/fsh/examples/Phenopacket_DevelopmentalDelay.fsh new file mode 100644 index 000000000..5f16f027a --- /dev/null +++ b/input/fsh/examples/Phenopacket_DevelopmentalDelay.fsh @@ -0,0 +1,31 @@ +Instance: DevelopmentalDelay +InstanceOf: Phenopacket +Description: "Example use case for a child with undiagnosed developmental delay" +* identifier.value = "id.treatment.1" +* status = #preliminary "preliminary" +* type = $LOINC#11516-2 "Physician Episode of care medical records" +* date = "2018-03-16" +* title = "Phenopacket (static snapshot of clinical findings to support differential diagnosis of a child with developmental delay)." +* author = Reference(PeterGeneticist) +* subject = Reference(Proband1) +* section[phenotypic_features].entry[+] = Reference(longPhiltrum) +* section[phenotypic_features].entry[+] = Reference(microphthalmia) +* section[phenotypic_features].entry[+] = Reference(retinalDetachment) +* section[phenotypic_features].entry[+] = Reference(tga) +* section[phenotypic_features].entry[+] = Reference(reducedVisualAcuity) +* section[phenotypic_features].entry[+] = Reference(lowSetEars) +* section[phenotypic_features].entry[+] = Reference(globalDevelopmentalDelay) +* section[phenotypic_features].entry[+] = Reference(muscleWeakness) +* section[phenotypic_features].entry[+] = Reference(hypotonia) +* section[phenotypic_features].entry[+] = Reference(amyotrophy) +* section[phenotypic_features].entry[+] = Reference(fiberSizeVariability) +* section[biosamples].entry[+] = Reference(muscleBiopsy) +* section[diseases].entry[0] = Reference(intellectualDisabilityDisease) + + + + + + + + diff --git a/input/fsh/examples/PhenopacketsGenomicInterpretation_PhenopacketsGenomicInterpretationExample02.fsh b/input/fsh/examples/PhenopacketsGenomicInterpretation_PhenopacketsGenomicInterpretationExample02.fsh new file mode 100644 index 000000000..3e39652ac --- /dev/null +++ b/input/fsh/examples/PhenopacketsGenomicInterpretation_PhenopacketsGenomicInterpretationExample02.fsh @@ -0,0 +1,17 @@ +Instance: PhenopacketsGenomicInterpretationExample02 +InstanceOf: PhenopacketsGenomicInterpretation // we may use the URL later to refer to this profile +Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors +Title: "Phenopackets Genomic Interpretation Example-2" +Description: "This is an example of phenopackets-variant which is a phenopackets profile of + the genomics reporting Genomics Report profile. + It represents phenopackets GenomicInterpretation building block, i.e., the + interpretation for an individual variant or gene." +* identifier.value = "02" +* specimen = Reference(phenopacketSpecimenExample01) // we may need to use a real specimen example +* subject = Reference(phenopacketPatientExample01) +* category[Genetics] = http://terminology.hl7.org/CodeSystem/v2-0074#GE "Genetics" +* modifierExtension[interpretationStatus].valueCodeableConcept = PPIS#0 "UNKNOWN_STATUS" +* result[variant] = Reference(PhenopacketsVariantExample01) +* conclusion = "A rare genetic form of obesity characterized by morbid obesity, hypertension, type 2 diabetes mellitus and dyslipidemia leading to early coronary disease, myocardial infarction and congestive heart failure. Intellectual disability and decreased sperm counts or azoospermia have also been reported." +* conclusionCode.coding = $sct#783549006 "Obesity due to centrosomal protein 19 deficiency (disorder)" +* code = http://loinc#123 "some loinc code" diff --git a/input/fsh/examples/PhenopacketsVariant_PhenopacketsVariantExample01.fsh b/input/fsh/examples/PhenopacketsVariant_PhenopacketsVariantExample01.fsh new file mode 100644 index 000000000..411a76078 --- /dev/null +++ b/input/fsh/examples/PhenopacketsVariant_PhenopacketsVariantExample01.fsh @@ -0,0 +1,26 @@ +Instance: PhenopacketsVariantExample01 +InstanceOf: PhenopacketsVariant // we may use the URL later to refer to this profile +Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors +Title: "Phenopackets Variant Example-1" +Description: "This is an example of phenopackets-genomic-interpretation + which is a phenopackets profile of the genomics reporting Variant profile. + It represents phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, + and VariantInterpretation building blocks." +* status = #final + +Instance: PhenopacketsGenomicInterpretationExample01 +InstanceOf: PhenopacketsGenomicInterpretation // we may use the URL later to refer to this profile +Usage: #example // Should it be #inline? It is now #example to avoid any SUSHI compilation errors +Title: "Phenopackets Genomic Interpretation Example-1" +Description: "This is an example of phenopackets-variant which is a phenopackets profile of + the genomics reporting Genomics Report profile. + It represents phenopackets GenomicInterpretation building block, i.e., the + interpretation for an individual variant or gene." +* specimen = Reference(phenopacketSpecimenExample01) // we may need to use a real specimen example +* subject = Reference(phenopacketPatientExample01) +* category[Genetics] = http://terminology.hl7.org/CodeSystem/v2-0074#GE "Genetics" +* modifierExtension[interpretationStatus].valueCodeableConcept = PPIS#0 "UNKNOWN_STATUS" +* result[variant] = Reference(PhenopacketsVariantExample01) +* conclusion = "The detected variant is Likely-Pathogenic of Pfeiffer syndrome" +* conclusionCode.coding = $sct#70410008 "Acrocephalosyndactyly type V (disorder)" +* code = http://loinc#123 "some loinc code" diff --git a/input/fsh/examples/PhenotypicFeature_CHF-with-severity.fsh b/input/fsh/examples/PhenotypicFeature_CHF-with-severity.fsh new file mode 100644 index 000000000..afaf51d64 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_CHF-with-severity.fsh @@ -0,0 +1,10 @@ +Instance: CHF-with-severity +InstanceOf: PhenotypicFeature +Description: "PhenotypicFeature Example for severe Low-output congestive heart failure" +* status = #final "final" +* subject = Reference(example-patient) +* code = $hpo#HP:0009805 "Low-output congestive heart failure" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" +* effectiveDateTime = "2018-03-06" +* component.code = $hpo#HP:0012824 "Severity" +* component.valueCodeableConcept = $hpo#HP:0012828 "Severe" diff --git a/input/fsh/examples/PhenotypicFeature_MVP-with-onset.fsh b/input/fsh/examples/PhenotypicFeature_MVP-with-onset.fsh new file mode 100644 index 000000000..6eab63bb9 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_MVP-with-onset.fsh @@ -0,0 +1,8 @@ +Instance: MVP-with-onset +InstanceOf: PhenotypicFeature +Description: "PhenotypicFeature Example for mitral value prolapse with onset" +* status = #final "final" +* subject = Reference(example-patient) +* code = $hpo#HP:0001634 "Mitral valve prolapse" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" +* effectiveDateTime = "2018-03-06" diff --git a/input/fsh/examples/PhenotypicFeature_Polydactyly-with-modifier.fsh b/input/fsh/examples/PhenotypicFeature_Polydactyly-with-modifier.fsh new file mode 100644 index 000000000..66ba2271a --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_Polydactyly-with-modifier.fsh @@ -0,0 +1,10 @@ +Instance: Polydactyly-with-modifier +InstanceOf: PhenotypicFeature +Description: "Bilateral postaxial Polydactyly, example to demonstrate use of Clinical Modifier" +* status = #final "final" +* subject = Reference(example-patient) +* code = $hpo#HP:0001162 "Postaxial hand polydactyly" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" +* effectiveDateTime = "2022-09-18" +* component.code = $hpo#HP:0012823 "Clinical modifier" +* component.valueCodeableConcept = $hpo#HP:0012832 "Bilateral" diff --git a/input/fsh/examples/PhenotypicFeature_amyotrophy.fsh b/input/fsh/examples/PhenotypicFeature_amyotrophy.fsh new file mode 100644 index 000000000..7ef7a53e1 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_amyotrophy.fsh @@ -0,0 +1,7 @@ +Instance: amyotrophy +InstanceOf: PhenotypicFeature +Description: "Skeletal muscle atrophy (HP:0003202)" +* status = #final "Final" +* subject = Reference(Proband1) +* code = $hpo#HP:0003202 "Skeletal muscle atrophy" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_arachnodactyly.fsh b/input/fsh/examples/PhenotypicFeature_arachnodactyly.fsh new file mode 100644 index 000000000..9a428ad30 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_arachnodactyly.fsh @@ -0,0 +1,7 @@ +Instance: arachnodactyly +InstanceOf: PhenotypicFeature +Description: "PhenotypicFeature Example for arachnodactyly" +* status = #final "final" +* subject = Reference(example-patient) +* code = $hpo#HP:0001166 "Arachnodactyly" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_fiberSizeVariability.fsh b/input/fsh/examples/PhenotypicFeature_fiberSizeVariability.fsh new file mode 100644 index 000000000..2bbcc1d9d --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_fiberSizeVariability.fsh @@ -0,0 +1,8 @@ +Instance: fiberSizeVariability +InstanceOf: PhenotypicFeature +Description: "Increased variability in muscle fiber diameter (HP:0003557)" +* id = "hp.0003557" +* status = #final "Final" +* focus = Reference(muscleBiopsy) +* code = $hpo#HP:0003557 "Increased variability in muscle fiber diameter" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_globalDevelopmentalDelay.fsh b/input/fsh/examples/PhenotypicFeature_globalDevelopmentalDelay.fsh new file mode 100644 index 000000000..c2fd9b5ab --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_globalDevelopmentalDelay.fsh @@ -0,0 +1,7 @@ +Instance: globalDevelopmentalDelay +InstanceOf: PhenotypicFeature +Description: "Global developmental delay (HP:0001263)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0001263 "Global developmental delay" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_hypotonia.fsh b/input/fsh/examples/PhenotypicFeature_hypotonia.fsh new file mode 100644 index 000000000..8bbecf2f5 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_hypotonia.fsh @@ -0,0 +1,7 @@ +Instance: hypotonia +InstanceOf: PhenotypicFeature +Description: "Hypotonia (HP:0001252)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0001252 "Hypotonia" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_longPhiltrum.fsh b/input/fsh/examples/PhenotypicFeature_longPhiltrum.fsh new file mode 100644 index 000000000..bef6cc09a --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_longPhiltrum.fsh @@ -0,0 +1,7 @@ +Instance: longPhiltrum +InstanceOf: PhenotypicFeature +Description: "Long philtrum (HP:0000343)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0000343 "Long philtrum" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_lowSetEars.fsh b/input/fsh/examples/PhenotypicFeature_lowSetEars.fsh new file mode 100644 index 000000000..479ebb53a --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_lowSetEars.fsh @@ -0,0 +1,7 @@ +Instance: lowSetEars +InstanceOf: PhenotypicFeature +Description: "Low-set ears (HP:0000369)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0000369 "Reduced visual acuity" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_lvdysfunction-excluded.fsh b/input/fsh/examples/PhenotypicFeature_lvdysfunction-excluded.fsh new file mode 100644 index 000000000..5a631243c --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_lvdysfunction-excluded.fsh @@ -0,0 +1,7 @@ +Instance: lvdysfunction-excluded +InstanceOf: PhenotypicFeature +Description: "PhenotypicFeature Example for exclusion of LV dysfunction" +* status = #final "final" +* subject = Reference(example-patient) +* code = $hpo#HP:0025168 "Left ventricular diastolic dysfunction" +* valueCodeableConcept = $LOINC#LA9634-2 "Absent" diff --git a/input/fsh/examples/PhenotypicFeature_microphthalmia.fsh b/input/fsh/examples/PhenotypicFeature_microphthalmia.fsh new file mode 100644 index 000000000..184302d85 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_microphthalmia.fsh @@ -0,0 +1,7 @@ +Instance: microphthalmia +InstanceOf: PhenotypicFeature +Description: "Long philtrum (HP:0000568)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0000568 "Microphthalmia" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_muscleWeakness.fsh b/input/fsh/examples/PhenotypicFeature_muscleWeakness.fsh new file mode 100644 index 000000000..850743cc2 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_muscleWeakness.fsh @@ -0,0 +1,7 @@ +Instance: muscleWeakness +InstanceOf: PhenotypicFeature +Description: "Muscle weakness (HP:0001324)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0001324 "Muscle weakness" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_reducedVisualAcuity.fsh b/input/fsh/examples/PhenotypicFeature_reducedVisualAcuity.fsh new file mode 100644 index 000000000..5202f0cba --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_reducedVisualAcuity.fsh @@ -0,0 +1,7 @@ +Instance: reducedVisualAcuity +InstanceOf: PhenotypicFeature +Description: "Reduced visual acuity (HP:0007663)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0007663 "Reduced visual acuity" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_retinalDetachment.fsh b/input/fsh/examples/PhenotypicFeature_retinalDetachment.fsh new file mode 100644 index 000000000..fc070ec6d --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_retinalDetachment.fsh @@ -0,0 +1,7 @@ +Instance: retinalDetachment +InstanceOf: PhenotypicFeature +Description: "Retinal detachment (HP:0000541)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0000541 "Retinal detachment" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/PhenotypicFeature_tga.fsh b/input/fsh/examples/PhenotypicFeature_tga.fsh new file mode 100644 index 000000000..0da087140 --- /dev/null +++ b/input/fsh/examples/PhenotypicFeature_tga.fsh @@ -0,0 +1,7 @@ +Instance: tga +InstanceOf: PhenotypicFeature +Description: "Transposition of the great arteries (HP:0001669)" +* status = #final "final" +* subject = Reference(Proband1) +* code = $hpo#HP:0001669 "Transposition of the great arteries" +* valueCodeableConcept = $LOINC#LA9633-4 "Present" diff --git a/input/fsh/examples/Practitioner_PeterGeneticist.fsh b/input/fsh/examples/Practitioner_PeterGeneticist.fsh new file mode 100644 index 000000000..fafa62566 --- /dev/null +++ b/input/fsh/examples/Practitioner_PeterGeneticist.fsh @@ -0,0 +1,16 @@ +Instance: PeterGeneticist +InstanceOf: Practitioner +Description: "Extended example: example practitioner" +* identifier.value = "practitioner.id1" +* name.family = "Geneticist" +* name.given[0] = "Peter" +* name.prefix[0] = "Dr." +* address.use = #work +* address.line[0] = "123 Yellow Brick Drive" +* address.city = "Anytown" +* address.state = "MA" +* address.postalCode = "12345" +* address.country = "US" +* gender = #male +* qualification.code = http://terminology.hl7.org/CodeSystem/v2-0360#MD +* qualification.code.coding[0].version = "2.7" diff --git a/input/fsh/examples/Practitioner_PhenopacketPractitionerExample01.fsh b/input/fsh/examples/Practitioner_PhenopacketPractitionerExample01.fsh new file mode 100644 index 000000000..8617773c1 --- /dev/null +++ b/input/fsh/examples/Practitioner_PhenopacketPractitionerExample01.fsh @@ -0,0 +1,12 @@ +Instance: PhenopacketPractitionerExample01 +InstanceOf: Practitioner +Usage: #example +Title: "phenopacket Practitioner Example01" +Description: "This is an incomplete example that used as + a placeholder for a curated Practitioner example" +* identifier.value = "03" +* identifier.use = #temp +* text.status = #generated +* text.div = "
This is an incomplete example that used as + a placeholder for a curated Practitioner example
" +* name.text = "John T. Practitioner" diff --git a/input/fsh/examples/Specimen_phenopacketSpecimenExample01.fsh b/input/fsh/examples/Specimen_phenopacketSpecimenExample01.fsh new file mode 100644 index 000000000..671feba18 --- /dev/null +++ b/input/fsh/examples/Specimen_phenopacketSpecimenExample01.fsh @@ -0,0 +1,12 @@ +Instance: phenopacketSpecimenExample01 +InstanceOf: Specimen +Usage: #example +Title: "phenopacket Specimen Example01" +Description: "This is an incomplete example that used as + a placeholder for a curated specimen example" +* identifier.value = "01" +* identifier.use = #temp +* text.status = #generated +* text.div = "
This is an incomplete example that used as + a placeholder for a curated specimen example
" +* subject = Reference(phenopacketPatientExample01) diff --git a/input/fsh/EX_Treatment.fsh b/input/fsh/examples/Treatment_losartan.fsh similarity index 100% rename from input/fsh/EX_Treatment.fsh rename to input/fsh/examples/Treatment_losartan.fsh diff --git a/input/fsh/extensions.fsh b/input/fsh/extensions.fsh deleted file mode 100644 index 88ace7e9f..000000000 --- a/input/fsh/extensions.fsh +++ /dev/null @@ -1,169 +0,0 @@ -Extension: CodedOnset -Id: CodedOnset -Title: "Coded Onset" -Description: "The onset of a disease using an ontology class." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Condition" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from Onset (required) - -Extension: DiagnosticMarker -Id: DiagnosticMarker -Title: "Diagnostic Marker" -Description: "Clinically relevant biomarkers. Most of the assays such as immunohistochemistry (IHC) are covered by the NCIT under the sub-hierarchy NCIT:C36292 (Laboratory Test Result), e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from DiagnosticMarker (example) - -Extension: HistologicalDiagnosis -Id: HistologicalDiagnosis -Title: "Histological Diagnosis" -Description: "This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis (which could be reported in the Phenopacket that contains this Biosample). Normal samples would be tagged with the term “NCIT:C38757”, “Negative Finding”." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from HistologicalDiagnosis (example) - - -Extension: KaryotypicSex -Id: KaryotypicSex -Title: "Karyotypic Sex" -Description: "Karyotypic sex of an individual (also known as chromosomal sex)." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2021-05-28T17:06:00-04:00" -* ^context.type = #element -* ^context.expression = "Patient" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from KaryotypicSex (required) - -Extension: MaterialSample -Id: MaterialSample -Title: "Material Sample" -Description: "Type of sample (diseases, control, etc.)" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2021-05-28T17:06:00-04:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept - -Extension: MeasurementExt -Id: MeasurementExt -Title: "Measurement (Biosample)" -Description: "Term representing a measurement made on a Biosample" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* value[x] only Reference(Measurement) - -Extension: Onset -Id: Onset -Title: "Onset" -Description: "Describes the age at which a phenotypic feature was first noticed or diagnosed." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Observation" -* value[x] only dateTime or string or Age or CodeableConcept or Period or Range - - -Extension: PathologicalStage -Id: PathologicalStage -Title: "Pathological Tumor Stage" -Description: "This element can be used if the phenopacket describes cancer. Tumor staging describes the extent of growth of cancer, including the tumor and, if applicable, affected lymph nodes and distant metastases. This element should not be confused with clinical stage." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from TumorStage (example) - -Extension: PathologicalTnmFinding -Id: PathologicalTnmFinding -Title: "Pathological TNM Finding" -Description: "Pathological TNM findings, if applicable. Corresponds to pathological_tnm_finding (GA4GH)" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from TumorStage (example) - - -Extension: PhenotypicFeatureExt -Id: PhenotypicFeatureExt -Title: "Phenotypic Feature (Biosample)" -Description: "Term representing phenotypic features of a Biosample" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* value[x] only Reference(PhenotypicFeature) - - -Extension: Taxonomy -Id: Taxonomy -Title: "Taxonomy" -Description: "Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Biosample" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from Taxonomy (required) - - -Extension: TumorGrade -Id: TumorGrade -Title: "Tumor Grade" -Description: "List of terms representing the tumor grade." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from TumorGrade (example) - -Extension: TumorProgression -Id: TumorProgression -Title: "Tumor Progression" -Description: "This field can be used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence. There are multiple ways of representing this using ontology terms, and the terms chosen should have a specific meaning that is application specific." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2020-02-14T16:13:10+10:00" -* ^context.type = #element -* ^context.expression = "Specimen" -* valueCodeableConcept only CodeableConcept -* valueCodeableConcept from TumorProgression (example) \ No newline at end of file diff --git a/input/fsh/extensions/CodedOnset.fsh b/input/fsh/extensions/CodedOnset.fsh new file mode 100644 index 000000000..85bcb7355 --- /dev/null +++ b/input/fsh/extensions/CodedOnset.fsh @@ -0,0 +1,12 @@ +Extension: CodedOnset +Id: CodedOnset +Title: "Coded Onset" +Description: "The onset of a disease using an ontology class." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Condition" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from Onset (required) diff --git a/input/fsh/extensions/DiagnosticMarker.fsh b/input/fsh/extensions/DiagnosticMarker.fsh new file mode 100644 index 000000000..688f43ce5 --- /dev/null +++ b/input/fsh/extensions/DiagnosticMarker.fsh @@ -0,0 +1,12 @@ +Extension: DiagnosticMarker +Id: DiagnosticMarker +Title: "Diagnostic Marker" +Description: "Clinically relevant biomarkers. Most of the assays such as immunohistochemistry (IHC) are covered by the NCIT under the sub-hierarchy NCIT:C36292 (Laboratory Test Result), e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from DiagnosticMarker (example) diff --git a/input/fsh/extensions/HistologicalDiagnosis.fsh b/input/fsh/extensions/HistologicalDiagnosis.fsh new file mode 100644 index 000000000..d72a0b6e9 --- /dev/null +++ b/input/fsh/extensions/HistologicalDiagnosis.fsh @@ -0,0 +1,12 @@ +Extension: HistologicalDiagnosis +Id: HistologicalDiagnosis +Title: "Histological Diagnosis" +Description: "This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis (which could be reported in the Phenopacket that contains this Biosample). Normal samples would be tagged with the term “NCIT:C38757”, “Negative Finding”." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from HistologicalDiagnosis (example) diff --git a/input/fsh/extensions/KaryotypicSex.fsh b/input/fsh/extensions/KaryotypicSex.fsh new file mode 100644 index 000000000..b04e00697 --- /dev/null +++ b/input/fsh/extensions/KaryotypicSex.fsh @@ -0,0 +1,12 @@ +Extension: KaryotypicSex +Id: KaryotypicSex +Title: "Karyotypic Sex" +Description: "Karyotypic sex of an individual (also known as chromosomal sex)." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2021-05-28T17:06:00-04:00" +* ^context.type = #element +* ^context.expression = "Patient" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from KaryotypicSex (required) diff --git a/input/fsh/extensions/MaterialSample.fsh b/input/fsh/extensions/MaterialSample.fsh new file mode 100644 index 000000000..ec34ecadc --- /dev/null +++ b/input/fsh/extensions/MaterialSample.fsh @@ -0,0 +1,11 @@ +Extension: MaterialSample +Id: MaterialSample +Title: "Material Sample" +Description: "Type of sample (diseases, control, etc.)" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2021-05-28T17:06:00-04:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept diff --git a/input/fsh/extensions/MeasurementExt.fsh b/input/fsh/extensions/MeasurementExt.fsh new file mode 100644 index 000000000..dce07eaeb --- /dev/null +++ b/input/fsh/extensions/MeasurementExt.fsh @@ -0,0 +1,11 @@ +Extension: MeasurementExt +Id: MeasurementExt +Title: "Measurement (Biosample)" +Description: "Term representing a measurement made on a Biosample" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* value[x] only Reference(Measurement) diff --git a/input/fsh/extensions/Onset.fsh b/input/fsh/extensions/Onset.fsh new file mode 100644 index 000000000..bbe516e26 --- /dev/null +++ b/input/fsh/extensions/Onset.fsh @@ -0,0 +1,11 @@ +Extension: Onset +Id: Onset +Title: "Onset" +Description: "Describes the age at which a phenotypic feature was first noticed or diagnosed." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Observation" +* value[x] only dateTime or string or Age or CodeableConcept or Period or Range diff --git a/input/fsh/extensions/PathologicalStage.fsh b/input/fsh/extensions/PathologicalStage.fsh new file mode 100644 index 000000000..cbec22842 --- /dev/null +++ b/input/fsh/extensions/PathologicalStage.fsh @@ -0,0 +1,12 @@ +Extension: PathologicalStage +Id: PathologicalStage +Title: "Pathological Tumor Stage" +Description: "This element can be used if the phenopacket describes cancer. Tumor staging describes the extent of growth of cancer, including the tumor and, if applicable, affected lymph nodes and distant metastases. This element should not be confused with clinical stage." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from TumorStage (example) diff --git a/input/fsh/extensions/PathologicalTnmFinding.fsh b/input/fsh/extensions/PathologicalTnmFinding.fsh new file mode 100644 index 000000000..3918e440c --- /dev/null +++ b/input/fsh/extensions/PathologicalTnmFinding.fsh @@ -0,0 +1,12 @@ +Extension: PathologicalTnmFinding +Id: PathologicalTnmFinding +Title: "Pathological TNM Finding" +Description: "Pathological TNM findings, if applicable. Corresponds to pathological_tnm_finding (GA4GH)" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from TumorStage (example) diff --git a/input/fsh/extensions/PhenotypicFeatureExt.fsh b/input/fsh/extensions/PhenotypicFeatureExt.fsh new file mode 100644 index 000000000..93606dd68 --- /dev/null +++ b/input/fsh/extensions/PhenotypicFeatureExt.fsh @@ -0,0 +1,11 @@ +Extension: PhenotypicFeatureExt +Id: PhenotypicFeatureExt +Title: "Phenotypic Feature (Biosample)" +Description: "Term representing phenotypic features of a Biosample" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* value[x] only Reference(PhenotypicFeature) diff --git a/input/fsh/extensions/Taxonomy.fsh b/input/fsh/extensions/Taxonomy.fsh new file mode 100644 index 000000000..f5c252964 --- /dev/null +++ b/input/fsh/extensions/Taxonomy.fsh @@ -0,0 +1,12 @@ +Extension: Taxonomy +Id: Taxonomy +Title: "Taxonomy" +Description: "Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Biosample" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from Taxonomy (required) diff --git a/input/fsh/extensions/TumorGrade.fsh b/input/fsh/extensions/TumorGrade.fsh new file mode 100644 index 000000000..718cd78cb --- /dev/null +++ b/input/fsh/extensions/TumorGrade.fsh @@ -0,0 +1,12 @@ +Extension: TumorGrade +Id: TumorGrade +Title: "Tumor Grade" +Description: "List of terms representing the tumor grade." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from TumorGrade (example) diff --git a/input/fsh/extensions/TumorProgression.fsh b/input/fsh/extensions/TumorProgression.fsh new file mode 100644 index 000000000..d4c42ae7e --- /dev/null +++ b/input/fsh/extensions/TumorProgression.fsh @@ -0,0 +1,12 @@ +Extension: TumorProgression +Id: TumorProgression +Title: "Tumor Progression" +Description: "This field can be used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence. There are multiple ways of representing this using ontology terms, and the terms chosen should have a specific meaning that is application specific." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2020-02-14T16:13:10+10:00" +* ^context.type = #element +* ^context.expression = "Specimen" +* valueCodeableConcept only CodeableConcept +* valueCodeableConcept from TumorProgression (example) diff --git a/input/fsh/extensions/acmg-pathogenicity-classification.fsh b/input/fsh/extensions/acmg-pathogenicity-classification.fsh new file mode 100644 index 000000000..a8d94b0ca --- /dev/null +++ b/input/fsh/extensions/acmg-pathogenicity-classification.fsh @@ -0,0 +1,10 @@ +Extension: AcmgPathogenicityClassification +Id: acmg-pathogenicity-classification +Title: "ACMG Pathogenicity Classification" +Description: "One of the five ACMG pathogenicity categories, default is UNCERTAIN_SIGNIFICANCE." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only CodeableConcept +* valueCodeableConcept 1..1 +* valueCodeableConcept from AcmgPathogenicityClassificationVS (required) diff --git a/input/fsh/extensions/additional-variant-identifier.fsh b/input/fsh/extensions/additional-variant-identifier.fsh new file mode 100644 index 000000000..7540ce497 --- /dev/null +++ b/input/fsh/extensions/additional-variant-identifier.fsh @@ -0,0 +1,9 @@ +//Declaring an extension for additional identifier of the variant +Extension: AdditionalVariantIdentifier +Id: additional-variant-identifier +Title: "Additional Variant Identifier" +Description: "Used to list of unique identifiers where available. If this is a dbSNP variant, component[dbSNP-id] should be used instead." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only Identifier diff --git a/input/fsh/extensions/filter-status.fsh b/input/fsh/extensions/filter-status.fsh new file mode 100644 index 000000000..4ce1160ff --- /dev/null +++ b/input/fsh/extensions/filter-status.fsh @@ -0,0 +1,9 @@ +// Declaring an extension for the filter status +Extension: FilterStatus +Id: filter-status +Title: "Filter Status" +Description: "Filter status: PASS if this position has passed all filters." // More informative description may need to be added. +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only CodeableConcept or string diff --git a/input/fsh/extensions/interpretation-status.fsh b/input/fsh/extensions/interpretation-status.fsh new file mode 100644 index 000000000..8c9822849 --- /dev/null +++ b/input/fsh/extensions/interpretation-status.fsh @@ -0,0 +1,12 @@ +Extension: InterpretationStatus +Id: interpretation-status +Title: "Interpretation Status" +Description: "Describes the conclusion made about the genomic interpretation." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only CodeableConcept +* valueCodeableConcept 1..1 +* valueCodeableConcept from InterpretationStatusVS (required) +* . ^isModifier = true +* . ^isModifierReason = "The interpretation status could be REJECTED which may affect how the whole interpretation is interpreted." diff --git a/input/fsh/extensions/molecule-context.fsh b/input/fsh/extensions/molecule-context.fsh new file mode 100644 index 000000000..c2201181b --- /dev/null +++ b/input/fsh/extensions/molecule-context.fsh @@ -0,0 +1,10 @@ +Extension: MoleculeContext +Id: molecule-context +Title: "Molecule Context" +Description: "The molecular context of the vrs variation." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only CodeableConcept +* valueCodeableConcept 1..1 +* valueCodeableConcept from MoleculeContextVS (required) diff --git a/input/fsh/extensions/phred-quality-score.fsh b/input/fsh/extensions/phred-quality-score.fsh new file mode 100644 index 000000000..e84ca3682 --- /dev/null +++ b/input/fsh/extensions/phred-quality-score.fsh @@ -0,0 +1,9 @@ +//Declaring an extension for Phred score of alternative alleles +Extension: PhredQualityScore +Id: phred-quality-score +Title: "Phred Quality Score" +Description: "Used to include Phred-scaled quality score for the assertion made in ALT." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only Quantity // Do you prefer another FHIR data type? // make it a floating point diff --git a/input/fsh/extensions/related-concept-id.fsh b/input/fsh/extensions/related-concept-id.fsh new file mode 100644 index 000000000..1c3781204 --- /dev/null +++ b/input/fsh/extensions/related-concept-id.fsh @@ -0,0 +1,10 @@ +//Declaring an extension for xrefs +Extension: RelatedConceptID +Id: related-concept-id +Title: "Related Concept ID" +Description: "Used to provide identifiers to alternative resources representing related, but not equivalent concepts, for example gene ortholog ids" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only Identifier +//* valueIdentifier 0..1 //We may not need to declare this diff --git a/input/fsh/extensions/therapeutic-actionability.fsh b/input/fsh/extensions/therapeutic-actionability.fsh new file mode 100644 index 000000000..b8f9476c0 --- /dev/null +++ b/input/fsh/extensions/therapeutic-actionability.fsh @@ -0,0 +1,10 @@ +Extension: TherapeuticActionability +Id: therapeutic-actionability +Title: "Therapeutic Actionability" +Description: "one of the five ACMG pathogenicity categories, or NOT_PROVIDED. The default is NOT_PROVIDED." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only CodeableConcept +* valueCodeableConcept 1..1 +* valueCodeableConcept from TherapeuticActionabilityVS (required) diff --git a/input/fsh/extensions/vcf-info.fsh b/input/fsh/extensions/vcf-info.fsh new file mode 100644 index 000000000..2614885ab --- /dev/null +++ b/input/fsh/extensions/vcf-info.fsh @@ -0,0 +1,8 @@ +Extension: VCFInfo +Id: vcf-info +Title: "VCF Info" +Description: "Additional information: Semicolon-separated series of additional information fields from VCF info field." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only string diff --git a/input/fsh/extensions/vrs-object.fsh b/input/fsh/extensions/vrs-object.fsh new file mode 100644 index 000000000..cfaf008d2 --- /dev/null +++ b/input/fsh/extensions/vrs-object.fsh @@ -0,0 +1,9 @@ +Extension: VrsObject +Id: vrs-object +Title: "VRS Object" +Description: "The VRS Variation object (Link: https://vrs.ga4gh.org/en/stable/)" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* value[x] only Attachment +* valueAttachment 1..1 diff --git a/input/fsh/instances.fsh b/input/fsh/instances.fsh deleted file mode 100644 index f5d078fcd..000000000 --- a/input/fsh/instances.fsh +++ /dev/null @@ -1,107 +0,0 @@ -Instance: karyotypic-sex-invalid-1 -InstanceOf: Observation -Title: "An INVALID karyotypic sex Observation instance." -Description: "An INVALID karyotypic sex Observation instance." -Usage: #example -* status = #final -* code = $GSSO#GSSO:000113 -* valueCodeableConcept = $observation-karyotypic-sex#XXW - -Instance: karyotypic-sex-valid-1 -InstanceOf: Observation -Title: "A VALID karyotypic sex Observation instance." -Description: "A VALID karyotypic sex Observation instance." -Usage: #example -* status = #final -* code = $GSSO#GSSO:000113 -* valueCodeableConcept = $observation-karyotypic-sex#XX - -Instance: phenotypic-abnormality-invalid-1 -InstanceOf: Observation -Title: "An INVALID phenotypic abnormality Observation example." -Description: "An INVALID phenotypic abnormality Observation example." -Usage: #example -//* extension.url = "http://github.com/phenopackets/core-ig/ig-tools/validation-error-count" -//* extension.valueInteger = 4 -* status = #final -* code = $hpo#HP:0001249 "Intellectual disability" -* code.text = "Intellectual disability" -* valueBoolean = true -* component[0].code = $hpo#HP:0012824 "Severity" -* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" -* component[+].code = $hpo#HP:0012824 "Severity" -* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" -* component[+].code = $hpo#HP:0012823 "Clinical modifier" -* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" -* component[+].code = $hpo#HP:0012823 "Clinical modifier" -* component[=].valueCodeableConcept = $hpo#HP:0031375 "Refractory" -* component[+].code = $hpo#HP:0012823 "Clinical modifier" -* component[=].valueCodeableConcept = $hpo#HP:999999999 "Non existant modifier" -* component[+].code = $hpo#HP:0003674 "Onset" -* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" -* component[+].code = $hpo#HP:0003674 "Onset" -* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" -* component[+].code = $OTHER#OTHER "Severity" -* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" - -//Instance: phenotypic-abnormality-invalid-meta-profile -//InstanceOf: Observation -//Usage: #example -//* status = #final -//* code = $hpo#HP:0001249 "Intellectual disability" -//* code.text = "Intellectual disability" -//* valueBoolean = true -//* component[0].code = $hpo#HP:0012824 "Severity" -//* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" -//* component[+].code = $hpo#HP:0012824 "Severity" -//* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" -//* component[+].code = $hpo#HP:0012823 "Clinical modifier" -//* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" -//* component[+].code = $hpo#HP:0012823 "Clinical modifier" -//* component[=].valueCodeableConcept = $hpo#HP:0031375 "Refractory" -//* component[+].code = $hpo#HP:0012823 "Clinical modifier" -//* component[=].valueCodeableConcept = $hpo#HP:999999999 "Non existant modifier" -//* component[+].code = $hpo#HP:0003674 "Onset" -//* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" -//* component[+].code = $hpo#HP:0003674 "Onset" -//* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" -//* component[+].code = $OTHER#OTHER "Severity" -//* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" - -Instance: phenotypic-abnormality-valid-1 -InstanceOf: Observation -Title: "A valid phenotypic abnormality Observation example." -Description: "A valid phenotypic abnormality Observation example." -Usage: #example -* status = #final -* code = $hpo#HP:0001249 "Intellectual disability" -* code.text = "Intellectual disability" -* valueBoolean = true -* component[0].code = $hpo#HP:0012824 "Severity" -* component[=].valueCodeableConcept = $hpo#HP:0012825 "Mild" -* component[+].code = $hpo#HP:0012823 "Clinical modifier" -* component[=].valueCodeableConcept = $hpo#HP:0410401 "Worse in evening" -* component[+].code = $hpo#HP:0003674 "Onset" -* component[=].valueCodeableConcept = $hpo#HP:0003577 "Congenital onset" -* component[+].code = $hpo#HP:0003674 "Onset" -* component[=].valueQuantity = 0 http://some/unit/system#Day "Day" -* component[+].code = $OTHER#OTHER "Severity" -* component[=].valueCodeableConcept = $OTHER#OTHERTHING "Mild" - - - -Instance: service-request-supporting-info -InstanceOf: SearchParameter -Usage: #definition -* insert SP_Publisher -* insert Version -* url = "http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info" -* name = "ServiceRequestSupportingInfo" -* status = #active -* description = "Search ServiceRequest by supporting resource parameters" -* code = #supporting-info -* base = #ServiceRequest -* type = #reference -* expression = "ServiceRequest.supportingInfo" -* target = #Bundle -* comparator = #eq \ No newline at end of file diff --git a/input/fsh/invariants/1.fsh b/input/fsh/invariants/1.fsh new file mode 100644 index 000000000..e69de29bb diff --git a/input/fsh/invariants/phenopackets-dbsnp-id-and-other-ids.fsh b/input/fsh/invariants/phenopackets-dbsnp-id-and-other-ids.fsh new file mode 100644 index 000000000..48ebfd08b --- /dev/null +++ b/input/fsh/invariants/phenopackets-dbsnp-id-and-other-ids.fsh @@ -0,0 +1,7 @@ +//Place-holder for dbSNP-id variation identifier vs other CURIE identifiers invariant +Invariant: phenopackets-dbsnp-id-and-other-ids +Description: "component-dbSNP-id SHAll be used to represent dbSNP-ids. For other ids, corresponding components + SHALL be used" +//Expression: "" +Severity: #error +//XPath: "" diff --git a/input/fsh/invariants/phenopackets-moleculeContext-align-with-result-component.fsh b/input/fsh/invariants/phenopackets-moleculeContext-align-with-result-component.fsh new file mode 100644 index 000000000..7b61bd1c5 --- /dev/null +++ b/input/fsh/invariants/phenopackets-moleculeContext-align-with-result-component.fsh @@ -0,0 +1,10 @@ +//Place-holder for an invariant that links variation components and molecule context extension +Invariant: phenopackets-moleculeContext-align-with-result-component +Description: "The extension[moleculeContext].value SHALL be aligned to the Variant results components for values + other than PPMC#0 'unspecified_molecule_context'. Where + - PPMC#1 'genomic' corresponds to variation-code; dna-chg; or genomic-dna-chg, + - PPMC#2 'transcript' corresponds to variation-code; or dna-chg; + - PPMC#3 'protein' corresponds to variation-code; or amino-acid-chg" +//Expression: "" +Severity: #error +//XPath: "" diff --git a/input/fsh/invariants/phenopackets-one-variation-identifier-component.fsh b/input/fsh/invariants/phenopackets-one-variation-identifier-component.fsh new file mode 100644 index 000000000..ca7501524 --- /dev/null +++ b/input/fsh/invariants/phenopackets-one-variation-identifier-component.fsh @@ -0,0 +1,9 @@ +Invariant: phenopackets-one-variation-identifier-component +Description: "Only one of the following components SHALL be used to describe the intended variation + - component:variation-code + - component:dna-chg + - component:genomic-dna-chg.valueCodeableConcept + - component:amino-acid-chg.valueCodeableConcept" +//Expression: "" +Severity: #error +//XPath: "" diff --git a/input/fsh/invariants/phenopackets-primary-and-alternate-ids-or-labels.fsh b/input/fsh/invariants/phenopackets-primary-and-alternate-ids-or-labels.fsh new file mode 100644 index 000000000..b50e8bf17 --- /dev/null +++ b/input/fsh/invariants/phenopackets-primary-and-alternate-ids-or-labels.fsh @@ -0,0 +1,12 @@ +//Place-holder for primary identifier and alternate identifiers invariant +/* This invariant is to be used with: + - VariationDescriptor.label+description and VariationDescriptor.alternateLabels + - GeneDescriptor.value_id+symbol and GeneDescriptor.alternate_symbols +*/ +Invariant: phenopackets-primary-and-alternate-ids-or-labels +Description: "primary ID SHALL be present in this component, while alternate id/lables and their associated ids/lables + SHALL be added to it, if present. They SHALL be add as additional codings within the valueCodeableConcept + of this element/component" +//Expression: "" +Severity: #warning //Is it better to be #error? +//XPath: "" diff --git a/input/fsh/invariants/phenopackets-subject-or-specimen-id.fsh b/input/fsh/invariants/phenopackets-subject-or-specimen-id.fsh new file mode 100644 index 000000000..951a78905 --- /dev/null +++ b/input/fsh/invariants/phenopackets-subject-or-specimen-id.fsh @@ -0,0 +1,5 @@ +Invariant: phenopackets-subject-or-specimen-id // we may change the name of this invariant to be numbered. It was just kept to clearly reflect its purpose. +Description: "subject.id and/or specimen.id SHALL be present" +//Expression: "subject[Patient].identifier.exists() or specimen[Specimen].identifier.exists()" // we may need to revise this in corresponding patient and biosample mappings +Severity: #error +//XPath: ""//this is optional diff --git a/input/fsh/profiles.fsh b/input/fsh/profiles.fsh deleted file mode 100644 index b5ca9c84b..000000000 --- a/input/fsh/profiles.fsh +++ /dev/null @@ -1,151 +0,0 @@ -Profile: Biosample -Parent: Specimen -Id: Biosample -Title: "Biosample" -Description: "A unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #active -* ^date = "2021-06-08T09:49:00-04:00" -* identifier 1..1 MS -* identifier ^short = "Corresponds to id (GA4GH), i.e., a specimen identifier" -* type MS -* type ^short = "Corresponds to sample_type (GA4GH)" -* subject only Reference(Patient) -* subject MS -* subject ^short = "Patient.identifier corresponds to individual_id (GA4GH)" -* note MS -* note ^short = "Corresponds to description (GA4GH)" -* collection.bodySite MS -* collection.bodySite ^short = "Anatomical collection site. Corresponds to sampled_tissue (GA4GH)" -* extension contains - Taxonomy named Taxonomy 0..1 MS and - HistologicalDiagnosis named HistologicalDiagnosis 0.. MS and - TumorProgression named TumorProgression 0..1 MS and - TumorGrade named TumorGrade 0.. MS and - PathologicalStage named PathologicalStage 0.. MS and - PathologicalTnmFinding named PathologicalTnmFinding 0.. MS and - DiagnosticMarker named DiagnosticMarker 0.. MS and - MaterialSample named MaterialSample 0..1 MS -* collection.collected[x] MS -* collection.collected[x] ^short = "Corresponds to time_of_collection (GA4GH)" -* processing.procedure MS -* processing.procedure ^short = "Corresponds to procedure (GA4GH)" - - - -Profile: Disease -Parent: Condition -Id: Disease -Title: "Disease profile" -Description: "This profile stipulates that a FHIR Condition must have a codeable concept that represents the disease. The concepts can be taken from various ontologies, but for rare-disease concepts, we recommend MONDO." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #active -* ^date = "2021-06-03T09:49:00-04:00" -//* extension contains -// CodedOnset named CodedOnset ..1 MS //and -// TumorStage named TumorStage ..1 MS -//* code MS -//* subject MS -//* onset[x] MS - -Profile: Individual -Parent: Patient -Id: Individual -Title: "Individual" -Description: "The subject of the Phenopacket is represented by an Individual element. This element intends to represent an individual human or other organism." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* ^date = "2021-05-28T17:06:00-04:00" -* extension contains - // AgeOrAgeRange named AgeOrAgeRange ..1 MS and - KaryotypicSex named KaryotypicSex 0..1 MS //and -// Taxonomy named Taxonomy ..1 MS -* identifier MS -* gender MS -* birthDate MS - - -Profile: Measurement -Parent: Observation -Id: Measurement -Title: "Measurement" -Description: "This profile defines the GA4GH Measurement element in terms of the FHIR Observation" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #active -* ^date = "2021-06-03T09:49:00-04:00" -* code 1..1 MS - -Profile: PhenotypicFeature -Parent: Observation -Id: PhenotypicFeature -Title: "Phenotypic Feature" -Description: "This profile defines the GA4GH PhenotypicFeature element in terms of the FHIR Observation" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #active -* ^date = "2021-06-03T09:49:00-04:00" -* code 1..1 MS -* value[x] only CodeableConcept -* value[x] from http://loinc.org/vs/LL1937-3 (required) -* value[x] 1..1 MS -* value[x] ^short = "LOINC code for presence absence" -* value[x] ^definition = "LOINC code for presence absence" -* specimen ..0 -* device ..0 -* referenceRange ..0 -* hasMember ..0 -* component MS -* component ^short = "GA4GH severity and modifiers should be coded as CodeableConcepts in the code field of the component" -* component ^slicing.discriminator.type = #pattern -* component ^slicing.discriminator.path = "code.coding" -* component ^slicing.rules = #open -* component ^slicing.description = "Severity of Phenotypic Feature" -* component contains - severity 0..1 -//* component[severity] ^short = "Severity of phenotypic feature" -* component[severity].code.coding = $hpo#HP:0012824 "Severity" -* component[severity].value[x] only CodeableConcept -* component[severity].value[x] from HpoSeverityVS -* component ^slicing.discriminator.type = #pattern -* component ^slicing.discriminator.path = "code.coding" -* component ^slicing.rules = #open -* component ^slicing.description = "Modifier of Phenotypic Feature" -* component ^slicing.ordered = false -* component contains - modifier 0.. -* component[modifier].code.coding = $hpo#HP:0012823 "Clinical modifier" -* component[severity].value[x] only CodeableConcept -* component[modifier].value[x] from PhenotypicModifierValueSet - - - - - - -Profile: Treatment -Parent: MedicationAdministration -Id: Treatment -Title: "Treatment" -Description: "This profile defines the GA4GH Treatment element in terms of the FHIR MedicationAdministration" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #active -* ^date = "2021-06-18T09:49:00-04:00" -* category MS -* category ^short = "Corresponds to drug_type (GA4GH)" -* medication[x] 1..1 MS -* effective[x] MS -* effective[x] ^short = "Information from effective and dosage is required for dose_intervals (GA4GH)" -* dosage MS -* dosage ^short = "Information from effective and dosage is required for dose_intervals (GA4GH)" -* dosage.route MS -* dosage.route ^short = "Corresponds to route_of_administration (GA4GH)" diff --git a/input/fsh/profiles/1.fsh b/input/fsh/profiles/1.fsh new file mode 100644 index 000000000..e69de29bb diff --git a/input/fsh/profiles/Biosample.fsh b/input/fsh/profiles/Biosample.fsh new file mode 100644 index 000000000..7bede5620 --- /dev/null +++ b/input/fsh/profiles/Biosample.fsh @@ -0,0 +1,34 @@ +Profile: Biosample +Parent: Specimen +Id: Biosample +Title: "Biosample" +Description: "A unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #active +* ^date = "2021-06-08T09:49:00-04:00" +* identifier 1..1 MS +* identifier ^short = "Corresponds to id (GA4GH), i.e., a specimen identifier" +* type MS +* type ^short = "Corresponds to sample_type (GA4GH)" +* subject only Reference(Patient) +* subject MS +* subject ^short = "Patient.identifier corresponds to individual_id (GA4GH)" +* note MS +* note ^short = "Corresponds to description (GA4GH)" +* collection.bodySite MS +* collection.bodySite ^short = "Anatomical collection site. Corresponds to sampled_tissue (GA4GH)" +* extension contains + Taxonomy named Taxonomy 0..1 MS and + HistologicalDiagnosis named HistologicalDiagnosis 0.. MS and + TumorProgression named TumorProgression 0..1 MS and + TumorGrade named TumorGrade 0.. MS and + PathologicalStage named PathologicalStage 0.. MS and + PathologicalTnmFinding named PathologicalTnmFinding 0.. MS and + DiagnosticMarker named DiagnosticMarker 0.. MS and + MaterialSample named MaterialSample 0..1 MS +* collection.collected[x] MS +* collection.collected[x] ^short = "Corresponds to time_of_collection (GA4GH)" +* processing.procedure MS +* processing.procedure ^short = "Corresponds to procedure (GA4GH)" diff --git a/input/fsh/profiles/Disease.fsh b/input/fsh/profiles/Disease.fsh new file mode 100644 index 000000000..99a760144 --- /dev/null +++ b/input/fsh/profiles/Disease.fsh @@ -0,0 +1,16 @@ +Profile: Disease +Parent: Condition +Id: Disease +Title: "Disease profile" +Description: "This profile stipulates that a FHIR Condition must have a codeable concept that represents the disease. The concepts can be taken from various ontologies, but for rare-disease concepts, we recommend MONDO." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #active +* ^date = "2021-06-03T09:49:00-04:00" +//* extension contains +// CodedOnset named CodedOnset ..1 MS //and +// TumorStage named TumorStage ..1 MS +//* code MS +//* subject MS +//* onset[x] MS diff --git a/input/fsh/profiles/Individual.fsh b/input/fsh/profiles/Individual.fsh new file mode 100644 index 000000000..8a7a844ac --- /dev/null +++ b/input/fsh/profiles/Individual.fsh @@ -0,0 +1,16 @@ +Profile: Individual +Parent: Patient +Id: Individual +Title: "Individual" +Description: "The subject of the Phenopacket is represented by an Individual element. This element intends to represent an individual human or other organism." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* ^date = "2021-05-28T17:06:00-04:00" +* extension contains + // AgeOrAgeRange named AgeOrAgeRange ..1 MS and + KaryotypicSex named KaryotypicSex 0..1 MS //and +// Taxonomy named Taxonomy ..1 MS +* identifier MS +* gender MS +* birthDate MS diff --git a/input/fsh/profiles/Measurement.fsh b/input/fsh/profiles/Measurement.fsh new file mode 100644 index 000000000..fe152a1aa --- /dev/null +++ b/input/fsh/profiles/Measurement.fsh @@ -0,0 +1,11 @@ +Profile: Measurement +Parent: Observation +Id: Measurement +Title: "Measurement" +Description: "This profile defines the GA4GH Measurement element in terms of the FHIR Observation" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #active +* ^date = "2021-06-03T09:49:00-04:00" +* code 1..1 MS diff --git a/input/fsh/phenopacketProfile.fsh b/input/fsh/profiles/Phenopacket.fsh similarity index 100% rename from input/fsh/phenopacketProfile.fsh rename to input/fsh/profiles/Phenopacket.fsh diff --git a/input/fsh/profiles/PhenotypicFeature.fsh b/input/fsh/profiles/PhenotypicFeature.fsh new file mode 100644 index 000000000..477d4576d --- /dev/null +++ b/input/fsh/profiles/PhenotypicFeature.fsh @@ -0,0 +1,42 @@ +Profile: PhenotypicFeature +Parent: Observation +Id: PhenotypicFeature +Title: "Phenotypic Feature" +Description: "This profile defines the GA4GH PhenotypicFeature element in terms of the FHIR Observation" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #active +* ^date = "2021-06-03T09:49:00-04:00" +* code 1..1 MS +* value[x] only CodeableConcept +* value[x] from http://loinc.org/vs/LL1937-3 (required) +* value[x] 1..1 MS +* value[x] ^short = "LOINC code for presence absence" +* value[x] ^definition = "LOINC code for presence absence" +* specimen ..0 +* device ..0 +* referenceRange ..0 +* hasMember ..0 +* component MS +* component ^short = "GA4GH severity and modifiers should be coded as CodeableConcepts in the code field of the component" +* component ^slicing.discriminator.type = #pattern +* component ^slicing.discriminator.path = "code.coding" +* component ^slicing.rules = #open +* component ^slicing.description = "Severity of Phenotypic Feature" +* component contains + severity 0..1 +//* component[severity] ^short = "Severity of phenotypic feature" +* component[severity].code.coding = $hpo#HP:0012824 "Severity" +* component[severity].value[x] only CodeableConcept +* component[severity].value[x] from HpoSeverityVS +* component ^slicing.discriminator.type = #pattern +* component ^slicing.discriminator.path = "code.coding" +* component ^slicing.rules = #open +* component ^slicing.description = "Modifier of Phenotypic Feature" +* component ^slicing.ordered = false +* component contains + modifier 0.. +* component[modifier].code.coding = $hpo#HP:0012823 "Clinical modifier" +* component[severity].value[x] only CodeableConcept +* component[modifier].value[x] from PhenotypicModifierValueSet diff --git a/input/fsh/profiles/Treatment.fsh b/input/fsh/profiles/Treatment.fsh new file mode 100644 index 000000000..87b12197f --- /dev/null +++ b/input/fsh/profiles/Treatment.fsh @@ -0,0 +1,19 @@ +Profile: Treatment +Parent: MedicationAdministration +Id: Treatment +Title: "Treatment" +Description: "This profile defines the GA4GH Treatment element in terms of the FHIR MedicationAdministration" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #active +* ^date = "2021-06-18T09:49:00-04:00" +* category MS +* category ^short = "Corresponds to drug_type (GA4GH)" +* medication[x] 1..1 MS +* effective[x] MS +* effective[x] ^short = "Information from effective and dosage is required for dose_intervals (GA4GH)" +* dosage MS +* dosage ^short = "Information from effective and dosage is required for dose_intervals (GA4GH)" +* dosage.route MS +* dosage.route ^short = "Corresponds to route_of_administration (GA4GH)" diff --git a/input/fsh/Phenopackets-Genomics-Profiles.fsh b/input/fsh/profiles/phenopackets-genomic-interpretation.fsh similarity index 77% rename from input/fsh/Phenopackets-Genomics-Profiles.fsh rename to input/fsh/profiles/phenopackets-genomic-interpretation.fsh index 235b7d4ac..f6cef17ee 100644 --- a/input/fsh/Phenopackets-Genomics-Profiles.fsh +++ b/input/fsh/profiles/phenopackets-genomic-interpretation.fsh @@ -1,21 +1,3 @@ -//we need to add the FHIR Clinical Genomics-Genomics Reporting Implementation Guide STU1 as a dependency -Profile: PhenopacketsVariant -Parent: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant // Genomics Reporting Variant profile -Id: phenopackets-variant -Title: "Phenopackets Variant" -Description: "A profile of Genomics Reporting Variant profile that represents relevant phenopackets building blocks." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^status = #draft // This would be changed later to active -* ^date = "2021-10-18T06:00:00-04:00" -//* ^publisher = "GA4GH Phenopacket Working Group" -//* ^contact.name = "Aly Khalifa" -//* ^short = "A phenopackets profile of the genomics reporting Variant profile. It represents - //phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, and VariantInterpretation building blocks." -//This is a placeholder for all Must-support elements (MS). Based on a team discussion, all elements should be MS. - - Profile: PhenopacketsGenomicInterpretation Parent: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report // Genomics Reporting Genomics Report profile Id: phenopackets-genomic-interpretation diff --git a/input/fsh/profiles/phenopackets-variant.fsh b/input/fsh/profiles/phenopackets-variant.fsh new file mode 100644 index 000000000..3377e29db --- /dev/null +++ b/input/fsh/profiles/phenopackets-variant.fsh @@ -0,0 +1,16 @@ +//we need to add the FHIR Clinical Genomics-Genomics Reporting Implementation Guide STU1 as a dependency +Profile: PhenopacketsVariant +Parent: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant // Genomics Reporting Variant profile +Id: phenopackets-variant +Title: "Phenopackets Variant" +Description: "A profile of Genomics Reporting Variant profile that represents relevant phenopackets building blocks." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^status = #draft // This would be changed later to active +* ^date = "2021-10-18T06:00:00-04:00" +//* ^publisher = "GA4GH Phenopacket Working Group" +//* ^contact.name = "Aly Khalifa" +//* ^short = "A phenopackets profile of the genomics reporting Variant profile. It represents + //phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, and VariantInterpretation building blocks." +//This is a placeholder for all Must-support elements (MS). Based on a team discussion, all elements should be MS. diff --git a/input/fsh/searchparameters/service-request-supporting-info.fsh b/input/fsh/searchparameters/service-request-supporting-info.fsh new file mode 100644 index 000000000..23a0dab98 --- /dev/null +++ b/input/fsh/searchparameters/service-request-supporting-info.fsh @@ -0,0 +1,15 @@ +Instance: service-request-supporting-info +InstanceOf: SearchParameter +Usage: #definition +* insert SP_Publisher +* insert Version +* url = "http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info" +* name = "ServiceRequestSupportingInfo" +* status = #active +* description = "Search ServiceRequest by supporting resource parameters" +* code = #supporting-info +* base = #ServiceRequest +* type = #reference +* expression = "ServiceRequest.supportingInfo" +* target = #Bundle +* comparator = #eq diff --git a/input/fsh/valueSets.fsh b/input/fsh/valueSets.fsh deleted file mode 100644 index 16cef05f5..000000000 --- a/input/fsh/valueSets.fsh +++ /dev/null @@ -1,186 +0,0 @@ -ValueSet: DiagnosticMarker -Id: DiagnosticMarker -Title: "Diagnostic Marker" -Description: "Codes to indicate clinically relevant bio markers." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* include codes from system $ncit where concept descendent-of #NCIT:C36292 - -ValueSet: HistologicalDiagnosis -Id: HistologicalDiagnosis -Title: "HistologicalDiagnosis" -Description: "Histological diagnosis codes from NCIT." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* include codes from system $ncit where concept descendent-of #NCIT:C28101 -* include codes from system $ncit where concept descendent-of #NCIT:C2991 - -ValueSet: KaryotypicSex -Id: KaryotypicSex -Title: "Karyotypic sex value set" -Description: "The karyotypic (chromosomal) sex of an individual" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2021-05-28T17:06:00-04:00" -* include codes from system KaryotypicSex - - -ValueSet: ObservationCategories -Id: observation-categories -Title: "Observation categories" -Description: "ValueSet description here" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* include codes from valueset $observation-category -* Categories#phenotype - - -ValueSet: PhenotypicAbnormalityValueSet -Id: phenotypic-abnormality -Title: "Phenotypic abnormality ValueSet" -Description: "ValueSet description here" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* include codes from system $ncit where concept descendent-of $hpo#HP:0000118 - -ValueSet: PhenotypicComponentValueSet -Id: phenotypic-component -Title: "Phenotypic component ValueSet" -Description: "ValueSet description here" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* $hpo#HP:0012823 -* $hpo#HP:0012824 -* $hpo#HP:0003674 - -ValueSet: PhenotypicModifierValueSet -Id: PhenotypicModifierValueSet -Title: "Phenotypic modifier ValueSet" -Description: "Human Phenotype Ontology (HPO) Clinical Modifier terms" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -//* ^url = "http://github.com/phenopackets/core-ig/ValueSet/phenotypic-modifier" -* insert ShareableValueSet -* ^experimental = false -* $hpo#HP:0012823 -* include codes from system $hpo where concept is-a #HP:0012824 - - -ValueSet: PhenotypicFeatureStatusValueSet -Id: phenotypicFeatureVS -Title: "Observation Codes for status of a PhenotypicFeature" -Description: "The LOINC codes for present if a feature is observed and absent if a feature was excluded." -* ^copyright = "This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* $LOINC#LA9633-4 "Present" -* $LOINC#LA9634-2 "Absent" - - - -ValueSet: Onset -Id: Onset -Title: "Onset ValueSet" -Description: "Set of HPO codes that denote the onset of a disease or phenotypic feature. The codes are descendants of Onset (HP:0003674) or from SNOMED_CT (282032007)." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* insert SCT-copyright -* ^experimental = false -* ^date = "2021-06-03T10:26:00-04:00" -* include codes from system $hpo where concept is-a #HP:0003674 -* include codes from system SNOMED_CT where concept descendent-of #282032007 - - -ValueSet: Taxonomy -Id: Taxonomy -Title: "Taxonomy" -Description: "Taxonomic identifiers of an organism." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* include codes from system $ncbitaxon - -ValueSet: TumorGrade -Id: TumorGrade -Title: "Tumor Grade" -Description: "Codes to indicate the grade of a tumor." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* include codes from system $ncit where concept descendent-of #NCIT:C28076 - -ValueSet: TumorProgression -Id: TumorProgression -Title: "Tumor Progression" -Description: "Codes to indicate if a specimen is from the primary tumor, a metastasis or a recurrence." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* $ncit#NCIT:C8509 "Primary Neoplasm" -* $ncit#NCIT:C3261 "Metastatic Neoplasm" -* $ncit#NCIT:C4798 "Recurrent Neoplasm" - -ValueSet: TumorStage -Id: TumorStage -Title: "Tumor Stage" -Description: "Codes to represent the stage of a tumor." -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2020-02-14T16:13:10+10:00" -* include codes from system $ncit where concept descendent-of #NCIT:C48232 - - -ValueSet: HpoSeverityVS -Id: HpoSeverity -Title: "Hpo Severity Value Set" -Description: "The HPO codes for phenotypic feature severity" -* insert Publisher -* insert SD-WG -* insert PR_CS_VS_Version -* insert ShareableValueSet -* ^experimental = false -* ^date = "2022-09-19T16:13:10+10:00" -// This would be equivalent to the following* include codes from system $hpo where concept descendent-of #hpo:0012824 -* $hpo#HP:0012828 "Severe" -* $hpo#HP:0012826 "Moderate" -* $hpo#HP:0012825 "Mild" -* $hpo#HP:0012827 "Borderline" -* $hpo#HP:0012829 "Profound" \ No newline at end of file diff --git a/input/fsh/valuesets/DiagnosticMarker.fsh b/input/fsh/valuesets/DiagnosticMarker.fsh new file mode 100644 index 000000000..0f5a74ba4 --- /dev/null +++ b/input/fsh/valuesets/DiagnosticMarker.fsh @@ -0,0 +1,11 @@ +ValueSet: DiagnosticMarker +Id: DiagnosticMarker +Title: "Diagnostic Marker" +Description: "Codes to indicate clinically relevant bio markers." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* include codes from system $ncit where concept descendent-of #NCIT:C36292 diff --git a/input/fsh/valuesets/HistologicalDiagnosis.fsh b/input/fsh/valuesets/HistologicalDiagnosis.fsh new file mode 100644 index 000000000..23957827c --- /dev/null +++ b/input/fsh/valuesets/HistologicalDiagnosis.fsh @@ -0,0 +1,12 @@ +ValueSet: HistologicalDiagnosis +Id: HistologicalDiagnosis +Title: "HistologicalDiagnosis" +Description: "Histological diagnosis codes from NCIT." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* include codes from system $ncit where concept descendent-of #NCIT:C28101 +* include codes from system $ncit where concept descendent-of #NCIT:C2991 diff --git a/input/fsh/valuesets/HpoSeverity.fsh b/input/fsh/valuesets/HpoSeverity.fsh new file mode 100644 index 000000000..b68d52670 --- /dev/null +++ b/input/fsh/valuesets/HpoSeverity.fsh @@ -0,0 +1,16 @@ +ValueSet: HpoSeverityVS +Id: HpoSeverity +Title: "Hpo Severity Value Set" +Description: "The HPO codes for phenotypic feature severity" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2022-09-19T16:13:10+10:00" +// This would be equivalent to the following* include codes from system $hpo where concept descendent-of #hpo:0012824 +* $hpo#HP:0012828 "Severe" +* $hpo#HP:0012826 "Moderate" +* $hpo#HP:0012825 "Mild" +* $hpo#HP:0012827 "Borderline" +* $hpo#HP:0012829 "Profound" diff --git a/input/fsh/valuesets/KaryotypicSex.fsh b/input/fsh/valuesets/KaryotypicSex.fsh new file mode 100644 index 000000000..6d5a0535f --- /dev/null +++ b/input/fsh/valuesets/KaryotypicSex.fsh @@ -0,0 +1,11 @@ +ValueSet: KaryotypicSex +Id: KaryotypicSex +Title: "Karyotypic sex value set" +Description: "The karyotypic (chromosomal) sex of an individual" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2021-05-28T17:06:00-04:00" +* include codes from system KaryotypicSex diff --git a/input/fsh/valuesets/Onset.fsh b/input/fsh/valuesets/Onset.fsh new file mode 100644 index 000000000..fc61c8b6e --- /dev/null +++ b/input/fsh/valuesets/Onset.fsh @@ -0,0 +1,13 @@ +ValueSet: Onset +Id: Onset +Title: "Onset ValueSet" +Description: "Set of HPO codes that denote the onset of a disease or phenotypic feature. The codes are descendants of Onset (HP:0003674) or from SNOMED_CT (282032007)." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* insert SCT-copyright +* ^experimental = false +* ^date = "2021-06-03T10:26:00-04:00" +* include codes from system $hpo where concept is-a #HP:0003674 +* include codes from system SNOMED_CT where concept descendent-of #282032007 diff --git a/input/fsh/valuesets/PhenotypicModifierValueSet.fsh b/input/fsh/valuesets/PhenotypicModifierValueSet.fsh new file mode 100644 index 000000000..110af18aa --- /dev/null +++ b/input/fsh/valuesets/PhenotypicModifierValueSet.fsh @@ -0,0 +1,12 @@ +ValueSet: PhenotypicModifierValueSet +Id: PhenotypicModifierValueSet +Title: "Phenotypic modifier ValueSet" +Description: "Human Phenotype Ontology (HPO) Clinical Modifier terms" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +//* ^url = "http://github.com/phenopackets/core-ig/ValueSet/phenotypic-modifier" +* insert ShareableValueSet +* ^experimental = false +* $hpo#HP:0012823 +* include codes from system $hpo where concept is-a #HP:0012824 diff --git a/input/fsh/valuesets/Taxonomy.fsh b/input/fsh/valuesets/Taxonomy.fsh new file mode 100644 index 000000000..296436ada --- /dev/null +++ b/input/fsh/valuesets/Taxonomy.fsh @@ -0,0 +1,11 @@ +ValueSet: Taxonomy +Id: Taxonomy +Title: "Taxonomy" +Description: "Taxonomic identifiers of an organism." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* include codes from system $ncbitaxon diff --git a/input/fsh/valuesets/TumorGrade.fsh b/input/fsh/valuesets/TumorGrade.fsh new file mode 100644 index 000000000..3ec3d3d9d --- /dev/null +++ b/input/fsh/valuesets/TumorGrade.fsh @@ -0,0 +1,11 @@ +ValueSet: TumorGrade +Id: TumorGrade +Title: "Tumor Grade" +Description: "Codes to indicate the grade of a tumor." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* include codes from system $ncit where concept descendent-of #NCIT:C28076 diff --git a/input/fsh/valuesets/TumorProgression.fsh b/input/fsh/valuesets/TumorProgression.fsh new file mode 100644 index 000000000..b1c3dea79 --- /dev/null +++ b/input/fsh/valuesets/TumorProgression.fsh @@ -0,0 +1,13 @@ +ValueSet: TumorProgression +Id: TumorProgression +Title: "Tumor Progression" +Description: "Codes to indicate if a specimen is from the primary tumor, a metastasis or a recurrence." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* $ncit#NCIT:C8509 "Primary Neoplasm" +* $ncit#NCIT:C3261 "Metastatic Neoplasm" +* $ncit#NCIT:C4798 "Recurrent Neoplasm" diff --git a/input/fsh/valuesets/TumorStage.fsh b/input/fsh/valuesets/TumorStage.fsh new file mode 100644 index 000000000..bf5ad9ef9 --- /dev/null +++ b/input/fsh/valuesets/TumorStage.fsh @@ -0,0 +1,11 @@ +ValueSet: TumorStage +Id: TumorStage +Title: "Tumor Stage" +Description: "Codes to represent the stage of a tumor." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^date = "2020-02-14T16:13:10+10:00" +* include codes from system $ncit where concept descendent-of #NCIT:C48232 diff --git a/input/fsh/valuesets/acmgPathogenicityClassification-vs.fsh b/input/fsh/valuesets/acmgPathogenicityClassification-vs.fsh new file mode 100644 index 000000000..7137655c3 --- /dev/null +++ b/input/fsh/valuesets/acmgPathogenicityClassification-vs.fsh @@ -0,0 +1,16 @@ +ValueSet: AcmgPathogenicityClassificationVS +Id: acmgPathogenicityClassification-vs +Title: "ACMG Pathogenicity Classification Value Set" +Description: "Describes the ACMG five-tier pathogenicity classification system (Richards et al., 2015, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/)." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" +* PPAPC#0 "NOT_PROVIDED" +* PPAPC#1 "BENIGN" +* PPAPC#2 "LIKELY_BENIGN" +* PPAPC#3 "UNCERTAIN_SIGNIFICANCE" +* PPAPC#4 "LIKELY_PATHOGENIC" +* PPAPC#5 "PATHOGENIC" diff --git a/input/fsh/valuesets/geno-ontology-allelic-state-vs.fsh b/input/fsh/valuesets/geno-ontology-allelic-state-vs.fsh new file mode 100644 index 000000000..3dc96d465 --- /dev/null +++ b/input/fsh/valuesets/geno-ontology-allelic-state-vs.fsh @@ -0,0 +1,10 @@ +ValueSet: GenoOntologyAllelicStateVS +Id: geno-ontology-allelic-state-vs +Title: "GENO Ontology Allelic State Value Set" +Description: "Descendent terms of GENO_0000875" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* include codes from system GENO where concept is-a GENO#GENO_0000875 diff --git a/input/fsh/valuesets/interpretationStatus-vs.fsh b/input/fsh/valuesets/interpretationStatus-vs.fsh new file mode 100644 index 000000000..fccc90003 --- /dev/null +++ b/input/fsh/valuesets/interpretationStatus-vs.fsh @@ -0,0 +1,15 @@ +ValueSet: InterpretationStatusVS +Id: interpretationStatus-vs +Title: "Interpretation Status Value Set" +Description: "Describes the conclusion made about the genomic interpretation." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" +* PPIS#0 "UNKNOWN_STATUS" +* PPIS#1 "REJECTED" +* PPIS#2 "CANDIDATE" +* PPIS#3 "CONTRIBUTORY" +* PPIS#4 "CAUSATIVE" diff --git a/input/fsh/valuesets/moleculeContext-vs.fsh b/input/fsh/valuesets/moleculeContext-vs.fsh new file mode 100644 index 000000000..841594d1d --- /dev/null +++ b/input/fsh/valuesets/moleculeContext-vs.fsh @@ -0,0 +1,14 @@ +ValueSet: MoleculeContextVS +Id: moleculeContext-vs +Title: "Molecule Context Value Set" +Description: "Describes The molecular context of the variant. Default is unspecified_molecule_context." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" +* PPMC#0 "unspecified_molecule_context" +* PPMC#1 "genomic" +* PPMC#2 "transcript" +* PPMC#3 "protein" diff --git a/input/fsh/valuesets/observation-categories.fsh b/input/fsh/valuesets/observation-categories.fsh new file mode 100644 index 000000000..28b857f2d --- /dev/null +++ b/input/fsh/valuesets/observation-categories.fsh @@ -0,0 +1,11 @@ +ValueSet: ObservationCategories +Id: observation-categories +Title: "Observation categories" +Description: "ValueSet description here" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* include codes from valueset $observation-category +* Categories#phenotype diff --git a/input/fsh/valuesets/phenotypic-abnormality.fsh b/input/fsh/valuesets/phenotypic-abnormality.fsh new file mode 100644 index 000000000..a1db700bf --- /dev/null +++ b/input/fsh/valuesets/phenotypic-abnormality.fsh @@ -0,0 +1,10 @@ +ValueSet: PhenotypicAbnormalityValueSet +Id: phenotypic-abnormality +Title: "Phenotypic abnormality ValueSet" +Description: "ValueSet description here" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* include codes from system $ncit where concept descendent-of $hpo#HP:0000118 diff --git a/input/fsh/valuesets/phenotypic-component.fsh b/input/fsh/valuesets/phenotypic-component.fsh new file mode 100644 index 000000000..3025f962c --- /dev/null +++ b/input/fsh/valuesets/phenotypic-component.fsh @@ -0,0 +1,12 @@ +ValueSet: PhenotypicComponentValueSet +Id: phenotypic-component +Title: "Phenotypic component ValueSet" +Description: "ValueSet description here" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* $hpo#HP:0012823 +* $hpo#HP:0012824 +* $hpo#HP:0003674 diff --git a/input/fsh/valuesets/phenotypicFeatureVS.fsh b/input/fsh/valuesets/phenotypicFeatureVS.fsh new file mode 100644 index 000000000..8105b66ee --- /dev/null +++ b/input/fsh/valuesets/phenotypicFeatureVS.fsh @@ -0,0 +1,12 @@ +ValueSet: PhenotypicFeatureStatusValueSet +Id: phenotypicFeatureVS +Title: "Observation Codes for status of a PhenotypicFeature" +Description: "The LOINC codes for present if a feature is observed and absent if a feature was excluded." +* ^copyright = "This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc" +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* $LOINC#LA9633-4 "Present" +* $LOINC#LA9634-2 "Absent" diff --git a/input/fsh/valuesets/sequence-ontology-structural-variant-vs.fsh b/input/fsh/valuesets/sequence-ontology-structural-variant-vs.fsh new file mode 100644 index 000000000..6dc2ec250 --- /dev/null +++ b/input/fsh/valuesets/sequence-ontology-structural-variant-vs.fsh @@ -0,0 +1,10 @@ +ValueSet: SequenceOntologyStructuralVariantVS +Id: sequence-ontology-structural-variant-vs +Title: "Sequence Ontology Structural Variant Value Set" +Description: "Descendent terms of SO:0001537." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* include codes from system SO where concept is-a SO#SO:0001537 diff --git a/input/fsh/valuesets/therapeuticActionability-vs.fsh b/input/fsh/valuesets/therapeuticActionability-vs.fsh new file mode 100644 index 000000000..7fef6d6a8 --- /dev/null +++ b/input/fsh/valuesets/therapeuticActionability-vs.fsh @@ -0,0 +1,13 @@ +ValueSet: TherapeuticActionabilityVS +Id: therapeuticActionability-vs +Title: "Therapeutic Actionability Value Set" +Description: "Describes the therapeutic actionability of the variant." +* insert Publisher +* insert SD-WG +* insert PR_CS_VS_Version +* insert ShareableValueSet +* ^experimental = false +* ^copyright = "This value set includes content from Phenopackets, which is copyright © 2016+ Global Alliance for Genomics and Health (GA4GH)" +* PPTA#0 "UNKNOWN_ACTIONABILITY" +* PPTA#1 "NOT_ACTIONABLE" +* PPTA#2 "ACTIONABLE"