diff --git a/res/rarelink_cdm_v2_0_0_datadictionary.csv b/res/rarelink_cdm_v2_0_0_datadictionary.csv new file mode 100644 index 00000000..b9441bce --- /dev/null +++ b/res/rarelink_cdm_v2_0_0_datadictionary.csv @@ -0,0 +1,976 @@ +Variable / Field Name,Form Name,Section Header,Field Type,Field Label,"Choices, Calculations, OR Slider Labels",Field Note,Text Validation Type OR Show Slider Number,Text Validation Min,Text Validation Max,Identifier?,Branching Logic (Show field only if...),Required Field?,Custom Alignment,Question Number (surveys only),Matrix Group Name,Matrix Ranking?,Field Annotation +record_id,rarelink_1_formal_criteria,RareLink - 1) Formal Criteria,text,Registry ID the of Individual,,,,,,,,,,,,, +snomed_422549004,rarelink_1_formal_criteria,,text,1.1 Pseudonym,,The (local) patient-related Identification code,,,,,,,,,,,"Variable: +SNOMED:422549004 | Pseudonym | +Choices: n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.identifier.value +- GA4GH Phenopacket Schema v2.0 Element: Individual.id" +snomed_399423000,rarelink_1_formal_criteria,,text,1.2 Date of Admission,,The date of admission or data capture of the individual,date_ymd,,,,,,,,,,"Variable: +SNOMED:399423000 | Date of admission (observable entity) | +Choices: n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Encounter.period.start +- GA4GH Phenopacket Schema v2.0 Element: Individual.time_at_last_encounter" +personal_information_descr,rarelink_2_personal_information,RareLink - 2) Personal Information,descriptive,"
+

Notes for entering information into the Personal Information sheet

+ +
+",,,,,,,,,,,,, +snomed_184099003,rarelink_2_personal_information,,text,2.1 Date of birth,,"The individual's date of birth. If the exact month or day is allowd to be captured or not known, select the 1st day of the month or the 1st month of the year, respectively.",date_ymd,,,,,,,,,,"Variable: +SNOMED:184099003 | Date of Birth | +Choices: n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.birthDate +- GA4GH Phenopacket Schema v2.0 Element: Individual.date_of_birth" +snomed_281053000,rarelink_2_personal_information,,dropdown,2.2 Sex at birth,"snomed_248152002, Female | snomed_248153007, Male | snomed_184115007, Patient sex unknown | snomed_32570691000036108, Intersex | snomed_1220561009, Not recorded",The individual's sex that was assigned at birth,,,,,,,,,,,"Variable: +SNOMED:281053000 | Sex at Birth | +Choices: +- SNOMED:248152002 | Female +- SNOMED:248153007 | Male +- SNOMED:184115007 | Patient sex unknown +- SNOMED:32570691000036108 | Intersex +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.extension:individual-recordedSexOrGender +- GA4GH Phenopacket Schema v2.0 Element: Individual.sex" +snomed_1296886006,rarelink_2_personal_information,,dropdown,2.3 Karyotypic Sex,"snomed_261665006, Unknown | snomed_734875008, XX | snomed_734876009, XY | snomed_80427008, X0 | snomed_65162001, XXY | snomed_35111009, XXX | snomed_403760006, XXYY | snomed_78317008, XXXY | snomed_10567003, XXXX | snomed_48930007, XYY | snomed_74964007, Other",The chromosomal sex of an individual,,,,,,,,,,,"Variable: +SNOMED:1296886006 | Karyotypic Sex | +Choices: +- SNOMED:261665006 | Unknown +- SNOMED:734875008 | XX +- SNOMED:734876009 | XY +- SNOMED:80427008 | X0 +- SNOMED:65162001 | XXY +- SNOMED:35111009 | XXX +- SNOMED:403760006 | XXYY +- SNOMED:78317008 | XXXY +- SNOMED:10567003 | XXXX +- SNOMED:48930007 | XYY +- SNOMED:74964007 | Other +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.value +- GA4GH Phenopacket Schema v2.0 Element: Individual.karyotypic_sex" +snomed_263495000,rarelink_2_personal_information,,dropdown,2.4 Gender Identity,"snomed_446141000124107, Female gender identity | snomed_446151000124109, Male gender identity | snomed_394743007, Gender unknown | snomed_33791000087105, Identifies as nonbinary gender | snomed_1220561009, Not recorded",The self-assigned gender of the individual,,,,,,,,,,,"Variable: +SNOMED:263495000 | Gender Identity | +Choices: +- SNOMED:446141000124107 | Female gender identity +- SNOMED:446151000124109 | Male gender identity +- SNOMED:394743007 | Gender unknown +- SNOMED:33791000087105 | Identifies as nonbinary gender +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.extension:individual-genderIdentity +- GA4GH Phenopacket Schema v2.0 Element: Individual.gender" +snomed_370159000,rarelink_2_personal_information,,text,2.5 Country of Birth,,The individual's country of birth. Please enter a two or three letter ISO3166 code which you can search in the link provided in the description above.,,,,,,,,,,,"Variable: +SNOMED:370159000 | Country of Birth | +Choices: ISO 3166 - 2 or 3 letter country code +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.extension:patient-birthPlace +- GA4GH Phenopacket Schema v2.0 Element: n/a" +patient_status_descr,rarelink_3_patient_status,RareLink - 3) Patient Status,descriptive,"
+

Notes for entering information into the Patient Status sheet

+ +
",,,,,,,,,,,,, +patient_status_date,rarelink_3_patient_status,,text,Date of Completion for the Sheet,,,date_ymd,,,,,,,,,, +snomed_278844005,rarelink_3_patient_status,,dropdown,3.1 Vital Status,"snomed_438949009, Alive | snomed_419099009, Dead | snomed_399307001, Unknown - Lost in follow-up | snomed_185924006, Unknown - Opted-out | snomed_261665006, Unknown - Other Reason",The individual’s general clinical status or vital status.,,,,,,,,,,,"Variable: +SNOMED:278844005 | Vital Status | +Choices: +- SNOMED:438949009 | Alive +- SNOMED:419099009 | Dead +- SNOMED:399307001 | Unknown - Lost in follow-up +- SNOMED:185924006 | Unknown - Opted-out +- SNOMED:261665006 | Unknown - Other Reason +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.deceased.deceasedBoolean or Observation.value +- GA4GH Phenopacket Schema v2.0 Element: Individual.VitalStatus.status" +snomed_398299004,rarelink_3_patient_status,,text,3.2 Time of Death,,"If deceased, the individual’s date of death. If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,[snomed_278844005] <> 'snomed_419099009',,,,,,"Variable: +SNOMED:398299004 | Time of Death | +Choices: n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Patient.deceasedDateTime +- GA4GH Phenopacket Schema v2.0 Element: Individual.VitalStatus.time_of_death" +snomed_184305005,rarelink_3_patient_status,,text,3.3 Cause of Death [ICD10CM],BIOPORTAL:ICD10CM,"If deceased, the individual’s primary cause of death (i.e. according to the death certificate).",,,,,[snomed_278844005] <> 'snomed_419099009',,,,,,"Variable: +SNOMED:184305005 | Cause of Death | +Choices: n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.value.coding.code +- GA4GH Phenopacket Schema v2.0 Element: Individual.VitalStatus.cause_of_death" +snomed_105727008,rarelink_3_patient_status,,dropdown,3.4 Age Category,"snomed_3658006, Infancy | snomed_713153009, Toddler | snomed_255398004, Childhood | snomed_263659003, Adolescence | snomed_41847000, Adulthood | snomed_303112003, Fetal period | snomed_419099009, Dead | snomed_261665006, Unknown",The individual's age category at the time of data capture (1.2).,,,,,,,,,,,"Variable: +SNOMED:105727008 | Age Category | +Choices: +- SNOMED:3658006 | Infancy +- SNOMED:713153009 | Toddler +- SNOMED:255398004 | Childhood +- SNOMED:263659003 | Adolescence +- SNOMED:41847000 | Adulthood +- SNOMED:303112003 | Fetal period +- SNOMED:419099009 | Dead +- SNOMED:261665006 | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.value.coding.code +- GA4GH Phenopacket Schema v2.0 Element: Individual.time_at_last_encounter.ontology_class" +snomed_412726003,rarelink_3_patient_status,,text,3.5 Length of Gestation at Birth [weeks+days],,"The duration of the pregnancy in weeks and days, from the first day of the last menstrual period to the day of delivery, formatted as XX+X (weeks+days).",,,,,,,,,,,"Variable: +SNOMED:412726003 | Length of Gestation at Birth [weeks+days] | +Choices: +- n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:weeks.valueQuantity and Observation.component:days.valueQuantity +- GA4GH Phenopacket Schema v2.0 Element: n/a" +snomed_723663001,rarelink_3_patient_status,,dropdown,3.6 Undiagnosed RD Case,"snomed_373066001, Yes | snomed_373067005, No",Identifies cases where an RD diagnosis has not been established.,,,,,,,,,,,"Variable: +SNOMED:723663001 | Undiagnosed RD Case | +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code (e.g., ORDO:616874 - Rare disorder without a determined diagnosis after full investigation) +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass (e.g., ORDO:616874 - Rare disorder without a determined diagnosis after full investigation)" +care_pathway_descr,rarelink_4_care_pathway,RareLink - 4) Care Pathway,descriptive,"
+

Notes for entering information into the Care Pathway sheet

+ +
",,,,,,,,,,,,, +hl7fhir_enc_period_start,rarelink_4_care_pathway,,text,4.1 Encounter Start,,"The beginning of an encounter of the individual. If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,,,,,,,"Variable: +HL7 FHIR:encounter.period.start | Encounter Start | +Choices: n/a +Version(s): +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: Encounter.period.start +- GA4GH Phenopacket Schema v2.0 Element: n/a" +hl7fhir_enc_period_end,rarelink_4_care_pathway,,text,4.2 Encounter End,,"The end of an encounter of the individual. If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,,,,,,,"Variable: +HL7 FHIR:encounter.period.end | Encounter End | +Choices: n/a +Version(s): +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: Encounter.period.end +- GA4GH Phenopacket Schema v2.0 Element: n/a" +snomed_305058001,rarelink_4_care_pathway,,dropdown,4.3 Encounter Status,"hl7fhir_planned, Planned | hl7fhir_arrived, Arrived | hl7fhir_triaged, Triaged | hl7fhir_in-progress, In Progress | hl7fhir_onleave, On Leave | hl7fhir_finished, Finished | hl7fhir_cancelled, Cancelled | hl7fhir_entered-in-error, Entered in Error | hl7fhir_unknown, Unknown",The status of an encounter of the individual at the time of data capture.,,,,,,,,,,,"Variable: +SNOMED:305058001 | Encounter Status | +Choices: +- SNOMED:planned | Planned +- SNOMED:arrived | Arrived +- SNOMED:triaged | Triaged +- SNOMED:in-progress | In Progress +- SNOMED:onleave | On Leave +- SNOMED:finished | Finished +- SNOMED:cancelled | Cancelled +- SNOMED:entered-in-error | Entered in Error +- SNOMED:unknown | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Encounter.status +- GA4GH Phenopacket Schema v2.0 Element: n/a" +hl7fhir_encounter_class,rarelink_4_care_pathway,,dropdown,4.4 Encounter Class,"hl7fhir_amb, Ambulatory | hl7fhir_imp, Inpatient | hl7fhir_obsenc, Observation | hl7fhir_emer, Emergency | hl7fhir_vr, Virtual | hl7fhir_hh, Home Health | hl7fhir_rdc, RD Specialist Center | snomed_261665006, Unknown",The class of an encounter of the individual at the time of data capture.,,,,,,,,,,,"Variable: +HL7 FHIR:encounter.class | Encounter Class | +Choices: +- HL7 FHIR:AMB | Ambulatory +- HL7 FHIR:IMP | Inpatient +- HL7 FHIR:OBSENC | Observation +- HL7 FHIR:EMER | Emergency +- HL7 FHIR:VR | Virtual +- HL7 FHIR:HH | Home Health +- HL7 FHIR:RDC | RD Specialist Center +- SNOMED:261665006 | Unknown +Version(s): +- HL7 FHIR Version 4.0.1 +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Encounter.class +- GA4GH Phenopacket Schema v2.0 Element: n/a" +disease_descr,rarelink_5_disease,RareLink - 5) Disease,descriptive,"
+

Notes for entering information into the Disease sheet

+ +
",,,,,,,,,,,,, +disease_coding,rarelink_5_disease,,dropdown,Please choose the encoding of the disease to be captured,"mondo, MONDO | ordo, ORDO | icd10cm, ICD10CM | icd11, ICD11 | omim, OMIM",We recommend using MONDO to capture diseases with,,,,,,,,,,, +snomed_64572001_mondo,rarelink_5_disease,,text,5.1 Disease [MONDO],BIOPORTAL:MONDO,"Please look up the MONDO code for the disease that the individual was affected by. If a genetic diagnosis or subtypes were diagnosed, please also provide the same MONDO code as you will use for the related variants in 6.1 Genetic Findings.",,,,,[disease_coding] = 'mondo',,,,,,"Variable: +SNOMED:64572001 | Disease +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass " +snomed_64572001_ordo,rarelink_5_disease,,text,5.1 Disease [ORDO],BIOPORTAL:ORDO,Please look up the ORDO code for the disease that the individual was affected by.,,,,,[disease_coding] = 'ordo',,,,,,"Variable: +SNOMED:64572001 | Disease +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass " +snomed_64572001_icd10cm,rarelink_5_disease,,text,5.1 Disease [ICD10CM],BIOPORTAL:ICD10CM,Please look up the ICD10CM code for the disease that the individual was affected by.,,,,,[disease_coding] = 'icd10cm',,,,,,"Variable: +SNOMED:64572001 | Disease +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass " +snomed_64572001_icd11,rarelink_5_disease,,text,5.1 Disease [ICD11],,Please enter the ICD11 code for the disease that the individual was affected by.,,,,,[disease_coding] = 'icd11',,,,,,"Variable: +SNOMED:64572001 | Disease +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass " +snomed_64572001_omim_p,rarelink_5_disease,,text,5.1 Disease [OMIM_P],BIOPORTAL:OMIM,"A disease that the individual was affected by. If a genetic diagnosis or subtypes were diagnosed, please also provide the same OMIM_p code as you will use for the related variants in 6.1 Genetic Findings.",,,,,[disease_coding] = 'omim',,,,,,"Variable: +SNOMED:64572001 | Disease +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Disease.term:OntologyClass " +loinc_99498_8,rarelink_5_disease,,dropdown,5.2 Verification Status,"hl7fhir_unconfirmed, Unconfirmed | hl7fhir_provisional, Provisional | hl7fhir_differential, Differential | hl7fhir_confirmed, Confirmed | hl7fhir_refuted, Refuted | hl7fhir_entered-in-error, Entered in Error",The verification status of the disease.,,,,,,,,,,,"Variable: +LOINC:99498-8 | Verification Status +Choices: +- HL7FHIR:unconfirmed | Unconfirmed +- HL7FHIR:provisional | Provisional +- HL7FHIR:differential | Differential +- HL7FHIR:confirmed | Confirmed +- HL7FHIR:refuted | Refuted +- HL7FHIR:entered-in-error | Entered in Error +Version(s): +- LOINC Version 2.77 +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.verificationStatus +- GA4GH Phenopacket Schema v2.0 Element: Disease.excluded " +snomed_424850005,rarelink_5_disease,,dropdown,5.3 Age at Onset,"snomed_118189007, Prenatal | snomed_3950001, Birth | snomed_410672004, Date | snomed_261665006, Unknown",The age at the onset of the first symptoms or signs of the disease.,,,,,,,,,,,"Variable: +SNOMED:424850005 | Age at Onset +Choices: +- SNOMED:118189007 | Prenatal +- SNOMED:3950001 | Birth +- SNOMED:410672004 | Date +- SNOMED:261665006 | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.onsetString or Observation.valueCodeableConcept +- GA4GH Phenopacket Schema v2.0 Element: Disease.onset " +snomed_298059007,rarelink_5_disease,,text,5.4 Date of Onset,,"The date at onset of first symptoms or signs of the disease. If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,,,,,,,"Variable: +SNOMED:298059007 | Date of Onset +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.onsetDateTime +- GA4GH Phenopacket Schema v2.0 Element: Disease.onset " +snomed_423493009,rarelink_5_disease,,dropdown,5.5 Age at Diagnosis,"snomed_118189007, Prenatal | snomed_3950001, Birth | snomed_410672004, Date | snomed_261665006, Unknown",The individual’s age when the diagnosis was made.,,,,,,,,,,,"Variable: +SNOMED:423493009 | Age at Diagnosis +Choices: +- SNOMED:118189007 | Prenatal +- SNOMED:3950001 | Birth +- SNOMED:410672004 | Date +- SNOMED:261665006 | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.valueCodeableConcept +- GA4GH Phenopacket Schema v2.0 Element: n/a " +snomed_432213005,rarelink_5_disease,,text,5.6 Date of Diagnosis,,"The date on which the disease was determined. If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,,,,,,,"Variable: +SNOMED:432213005 | Date of Diagnosis +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.recordedDate +- GA4GH Phenopacket Schema v2.0 Element: Disease.onset " +snomed_363698007,rarelink_5_disease,,text,5.7 Body Site [SNOMED CT],BIOPORTAL:SNOMEDCT,The specific body site affected by disease is encoded using all descendants of SCT Body Structure (123037004).,,,,,,,,,,,"Variable: +SNOMED:363698007 | Body Site +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.bodySite.coding:snomed-ct +- GA4GH Phenopacket Schema v2.0 Element: Disease.primary_site.OntologyClass " +snomed_263493007,rarelink_5_disease,,dropdown,5.8 Clinical Status,"hl7fhir_active, Active | hl7fhir_recurrence, Recurrence | hl7fhir_relapse, Relapse | hl7fhir_inactive, Inactive | hl7fhir_remission, Remission | hl7fhir_resolved, Resolved","The clinical status of the disease indicates whether it is active, inactive, or resolved.",,,,,,,,,,,"Variable: +SNOMED:263493007 | Clinical Status +Choices: +- HL7FHIR:active | Active +- HL7FHIR:recurrence | Recurrence +- HL7FHIR:relapse | Relapse +- HL7FHIR:inactive | Inactive +- HL7FHIR:remission | Remission +- HL7FHIR:resolved | Resolved +Version(s): +- SNOMED CT Version 23.2.0 +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.clinicalStatus +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.progress_status.ProgressStatus " +snomed_246112005,rarelink_5_disease,,dropdown,5.9 Severity,"snomed_24484000, Severe | snomed_6736007, Moderate | snomed_255604002, Mild",The severity of the disease is categorised by clinical evaluation.,,,,,,,,,,,"Variable: +SNOMED:246112005 | Severity +Choices: +- SNOMED:24484000 | Severe +- SNOMED:6736007 | Moderate +- SNOMED:255604002 | Mild +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.severity +- GA4GH Phenopacket Schema v2.0 Element: n/a " +genetic_findings_descr,rarelink_6_1_genetic_findings,RareLink - 6.1) Genetic Findings,descriptive,"
+

Notes for entering information into the Genetic Findings sheet

+ +
",,,,,,,,,,,,, +genetic_diagnosis_code,rarelink_6_1_genetic_findings,,dropdown,Please choose the corresponding code system for a genetic diagnosis related to the variant captured below.,"mondo, MONDO | omim, OMIM","If you want to link it to a specific Disease, please use the same code system.",,,,,,,,,,, +snomed_106221001_mondo,rarelink_6_1_genetic_findings,,text,6.1.1 Genomic Diagnosis [MONDO],BIOPORTAL:MONDO,The genetic finding of a variant can be linked to a disease in (5.1) if the same MONDO codes is used.,,,,,[genetic_diagnosis_code] = 'mondo',,,,,,"Variable: +SNOMED:106221001 | Genomic Diagnosis +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: [Suggested] : Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.Diagnosis.disease" +snomed_106221001_omim_p,rarelink_6_1_genetic_findings,,text,6.1.1 Genomic Diagnosis [OMIM_p],BIOPORTAL:OMIM,The genetic finding of a variant can be linked to a disease in (5.1) if the same OMIM codes is used.,,,,,[genetic_diagnosis_code] = 'omim',,,,,,"Variable: +SNOMED:106221001 | Genomic Diagnosis +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Condition.code +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.Diagnosis.disease +" +ga4gh_progress_status,rarelink_6_1_genetic_findings,,dropdown,6.1.2 Progress Status of Interpretation,"ga4gh_unknown_progress, No information is available about the diagnosis | ga4gh_in_progress, No diagnosis has been found to date but additional differential diagnostic work is in progress. | ga4gh_completed, The work on the interpretation is complete. | ga4gh_solved, The interpretation is complete and also considered to be a definitive diagnosis | ga4gh_unsolved, The interpretation is complete but no definitive diagnosis was found",​​The interpretation has a ProgressStatus that refers to the status of the attempted diagnosis.,,,,,,,,,,,"Variable: +GA4GH:progress_status | Progress Status of Interpretation +Choices: +GA4GH:UNKNOWN_PROGRESS | No information is available about the diagnosis +GA4GH:IN_PROGRESS | No diagnosis has been found to date but additional differential diagnostic work is in progress. +GA4GH:COMPLETED | The work on the interpretation is complete. +GA4GH:SOLVED | The interpretation is complete and also considered to be a definitive diagnosis +GA4GH:UNSOLVED | The interpretation is complete but no definitive diagnosis was found +Version(s): +- GA4GH Phenopacket Schema Version 2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: [Suggested] Condition.extension (VS: GA4GH) +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.progress_status" +ga4gh_interp_status,rarelink_6_1_genetic_findings,,dropdown,6.1.3 Interpretation Status,"ga4gh_unknown_status, No information is available about the status | ga4gh_rejected, The variant or gene reported here is interpreted not to be related to the diagnosis | ga4gh_candidate, The variant or gene reported here is interpreted to possibly be related to the diagnosis | ga4gh_contributory, The variant or gene reported here is interpreted to be related to the diagnosis | ga4gh_causative, The variant or gene reported here is interpreted to be causative of the diagnosis",An enumeration that describes the conclusion made about the genomic interpretation.,,,,,,,,,,,"Variable: +GA4GH:interpretation_status | Interpretation Status +Choices: +GA4GH:UNKNOWN_STATUS | No information is available about the status +GA4GH:REJECTED | The variant or gene reported here is interpreted not to be related to the diagnosis +GA4GH:CANDIDATE | The variant or gene reported here is interpreted to possibly be related to the diagnosis +GA4GH:CONTRIBUTORY | The variant or gene reported here is interpreted to be related to the diagnosis +GA4GH:CAUSATIVE | The variant or gene reported here is interpreted to be causative of the diagnosis +Version(s): +- GA4GH Phenopacket Schema Version 2.0 +Mapping: +- FHIR Expression v4.0.1: [Suggested] Condition.extension (VS: GA4GH) +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.GenomicInterpretation" +loinc_81304_8,rarelink_6_1_genetic_findings,,dropdown,6.1.4 Structural Variant Analysis Method,"loinc_la26406-1, Karyotyping | loinc_la26404-6, FISH | loinc_la26418-6, PCR | loinc_la26419-4, qPCR (real-time PCR) | loinc_la26400-4, SNP array | loinc_la26813-8, Restriction fragment length polymorphism (RFLP) | loinc_la26810-4, DNA hybridization | loinc_la26398-0, Sequencing | loinc_la26415-2, MLPA | loinc_la46-8, Other",The method used to analyse structural variants in the genome.,,,,,,,,,,,"Variable: +LOINC:81304-8 | Structural Variant Analysis Method +Choices: +LOINC:LA26406-1 | Karyotyping +LOINC:LA26404-6 | FISH +LOINC:LA26418-6 | PCR +LOINC:LA26419-4 | qPCR (real-time PCR) +LOINC:LA26400-4 | SNP array +LOINC:LA26813-8 | Restriction fragment length polymorphism (RFLP) +LOINC:LA26810-4 | DNA hybridization +LOINC:LA26398-0 | Sequencing +LOINC:LA26415-2 | MLPA +LOINC:LA46-8 | Other +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.method +- GA4GH Phenopacket Schema v2.0 Element: n/a" +loinc_62374_4,rarelink_6_1_genetic_findings,,dropdown,6.1.5 Reference Genome,"loinc_la14032-9, NCBI Build 34 (hg16) | loinc_la14029-5, GRCh37 (hg19) | loinc_la14030-3, NCBI Build 36.1 (hg18) | loinc_la14031-1, NCBI Build 35 (hg17) | loinc_la26806-2, GRCh38 (hg38)",The reference genome used for analysing the genetic variant.,,,,,,,,,,,"Variable: +LOINC:62374-4 | Reference Genome +Choices: +LOINC:LA14032-9 | NCBI Build 34 (hg16) +LOINC:LA14029-5 | GRCh37 (hg19) +LOINC:LA14030-3 | NCBI Build 36.1 (hg18) +LOINC:LA14031-1 | NCBI Build 35 (hg17) +LOINC:LA26806-2 | GRCh38 (hg38) +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: MolecularSequence.referenceSeqId +- GA4GH Phenopacket Schema v2.0 Element:" +loinc_lp7824_8,rarelink_6_1_genetic_findings,,text,6.1.6 Genetic Mutation String,,An unvalidated (HGVS) string that describes the variant change.,,,,,,,,,,,"Variable: +LOINC:LP7824-8 | Genetic Mutation String +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:Variant.valueString +- GA4GH Phenopacket Schema v2.0 Element: [...].VariantInterpretation.VariationDescriptor.Extension" +variant_expression,rarelink_6_1_genetic_findings,,dropdown,Please choose the type of the variant's validated HGVS expression,"ghgvs, Genomic DNA change [g.HGVS] | chgvs, Sequence DNA change [c.HGVS] | phgvs, Amino Acid Change [p.HGVS]",We recommend using sequence DNA change expressions (c.HGVS) if possible.,,,,,,,,,,, +loinc_81290_9,rarelink_6_1_genetic_findings,,text,6.1.7 Genomic DNA Change [g.HGVS],,The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression.,,,,,[variant_expression] = 'ghgvs',,,,,,"Variable: +LOINC:81290-9 | Genomic DNA Change +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:Variant.valueCode +- GA4GH Phenopacket Schema v2.0 Element: ""[...]VariantInterpretation.VariationDescriptor.Expression [+] [...].MoleculeContext""" +loinc_48004_6,rarelink_6_1_genetic_findings,,text,6.1.8 Sequence DNA Change [c.HGVS],,The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression,,,,,[variant_expression] = 'chgvs',,,,,,"Variable: +LOINC:48004-6 | Sequence DNA Change +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:Variant.valueCode +- GA4GH Phenopacket Schema v2.0 Element: [...]VariantInterpretation.VariationDescriptor.Expression [+] [...].MoleculeContext" +loinc_48005_3,rarelink_6_1_genetic_findings,,text,6.1.9 Amino Acid Change [p.HGVS],,The specific change in the amino acid sequence resulting from a genetic variant as a validated p.HGVS expression,,,,,[variant_expression] = 'phgvs',,,,,,"Variable: +LOINC:48005-3 | Amino Acid Change +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:AminoAcidChange +- GA4GH Phenopacket Schema v2.0 Element: [...]VariantInterpretation.VariationDescriptor.Expression [+] [...].MoleculeContext" +variant_validation,rarelink_6_1_genetic_findings,,radio,Are you sure the entered HGVS expression was validated using the variant validator? ,"yes, Yes - I'm sure | no, No, I need to check again",Please use the links above to ensure validation of the expression you entered!,,,,,"[loinc_81290_9] <> '' or +[loinc_48004_6] <> '' or +[loinc_48005_3] <> ''",y,,,,, +loinc_48018_6,rarelink_6_1_genetic_findings,,text,6.1.10 Gene [HGNC-NR],BIOPORTAL:HGNC-NR,The specific gene or genes that were analysed or identified in the study.,,,,,,,,,,,"Variable: +LOINC:48018-6 | Gene +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:Gene +- GA4GH Phenopacket Schema v2.0 Element: [...].GenomicInterpretation.GeneDescriptor.value_id" +loinc_48018_6_label,rarelink_6_1_genetic_findings,,text,6.1.10A Gene Label,,"Please enter the respective Gene label, e.g. 'BRAF'",,,,,[loinc_48018_6] <> '',y,,,,, +loinc_53034_5,rarelink_6_1_genetic_findings,,dropdown,6.1.11 Zygosity,"loinc_la6705-3, Homozygous | loinc_la6706-1, (simple) Heterozygous | loinc_la26217-2, Compound heterozygous | loinc_la26220-6, Double heterozygous | loinc_la6707-9, Hemizygous | loinc_la6703-8, Heteroplasmic | loinc_la6704-6, Homoplasmic | loinc_53034_5_other, Other",The zygosity of the genetic variant.,,,,,,,,,,,"Variable: +LOINC:53034-5 | Zygosity +Choices: +LOINC:LA6705-3 | Homozygous +LOINC:LA6706-1 | (simple) Heterozygous +LOINC:LA26217-2 | Compound heterozygous +LOINC:LA26220-6 | Double heterozygous +LOINC:LA6707-9 | Hemizygous +LOINC:LA6703-8 | Heteroplasmic +LOINC:LA6704-6 | Homoplasmic +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:geneticsAllele.State | VS: Allelic State +- GA4GH Phenopacket Schema v2.0 Element: [...].GenomicInterpretation.VariantInterpretation.variationDescriptor.AllelicState" +loinc_53034_5_other,rarelink_6_1_genetic_findings,,text,6.1.11A Zygosity - Other [LOINC],BIOPORTAL:LOINC,Please search for a different zygosity in LOINC.,,,,,[loinc_53034_5] = 'other',,,,,,"Variable: +LOINC:53034-5 | Zygosity +Choices: +LOINC:LA6705-3 | Homozygous +LOINC:LA6706-1 | (simple) Heterozygous +LOINC:LA26217-2 | Compound heterozygous +LOINC:LA26220-6 | Double heterozygous +LOINC:LA6707-9 | Hemizygous +LOINC:LA6703-8 | Heteroplasmic +LOINC:LA6704-6 | Homoplasmic +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:geneticsAllele.State | VS: Allelic State +- GA4GH Phenopacket Schema v2.0 Element: [...].GenomicInterpretation.VariantInterpretation.variationDescriptor.AllelicState" +loinc_48002_0,rarelink_6_1_genetic_findings,,dropdown,6.1.12 Genomic Source Class,"loinc_la6683-2, Germline | loinc_la6684-0, Somatic | loinc_la10429-1, Fetal | loinc_la18194-3, Likely germline | loinc_la18195-0, Likely somatic | loinc_la18196-8, Likely fetal | loinc_la18197-6, Unknown genomic origin | loinc_la26807-0, De novo","The classification of the genomic source, such as germline, somatic, or other origins.",,,,,,,,,,,"Variable: +LOINC:48002-0 | Genomic Source Class +Choices: +LOINC:LA6683-2 | Germline +LOINC:LA6684-0 | Somatic +LOINC:LA10429-1 | Fetal +LOINC:LA18194-3 | Likely germline +LOINC:LA18195-0 | Likely somatic +LOINC:LA18196-8 | Likely fetal +LOINC:LA18197-6 | Unknown genomic origin +LOINC:LA26807-0 | De novo +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:GenomicSourceClass +- GA4GH Phenopacket Schema v2.0 Element: n/a" +loinc_48019_4,rarelink_6_1_genetic_findings,,dropdown,6.1.13 DNA Change Type,"loinc_la9658-1, Wild type | loinc_la6692-3, Deletion | loinc_la6686-5, Duplication | loinc_la6687-3, Insertion | loinc_la6688-1, Insertion/Deletion | loinc_la6689-9, Inversion | loinc_la6690-7, Substitution | loinc_48019_4_other, Other","The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types.",,,,,,,,,,,"Variable: +LOINC:48019-4 | DNA Change Type +Choices: +LOINC:LA9658-1 | Wild type +LOINC:LA6692-3 | Deletion +LOINC:LA6686-5 | Duplication +LOINC:LA6687-3 | Insertion +LOINC:LA6688-1 | Insertion/Deletion +LOINC:LA6689-9 | Inversion +LOINC:LA6690-7 | Substitution +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Variant.type +- GA4GH Phenopacket Schema v2.0 Element: n/a" +loinc_48019_4_other,rarelink_6_1_genetic_findings,,text,6.1.13A DNA Change Type - Other [LOINC],BIOPORTAL:LOINC,Please search for a different DNA change typ in LOINC.,,,,,,,,,,,"Variable: +LOINC:48019-4 | DNA Change Type +Choices: +LOINC:LA9658-1 | Wild type +LOINC:LA6692-3 | Deletion +LOINC:LA6686-5 | Duplication +LOINC:LA6687-3 | Insertion +LOINC:LA6688-1 | Insertion/Deletion +LOINC:LA6689-9 | Inversion +LOINC:LA6690-7 | Substitution +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Variant.type +- GA4GH Phenopacket Schema v2.0 Element: n/a" +loinc_53037_8,rarelink_6_1_genetic_findings,,dropdown,6.1.14 Clinical Significance [ACMG],"loinc_la6668-3, Pathogenic | loinc_la26332-9, Likely pathogenic | loinc_la26333-7, Uncertain significance | loinc_la26334-5, Likely benign | loinc_la6675-8, Benign | loinc_la4489-6, Unknown","The clinical significance of the genetic variant, indicating its impact on health and disease.",,,,,,,,,,,"Variable: +LOINC:53037-8 | Clinical Significance [ACMG] +Choices: +LOINC:LA6668-3 | Pathogenic +LOINC:LA26332-9 | Likely pathogenic +LOINC:LA26333-7 | Uncertain significance +LOINC:LA26334-5 | Likely benign +LOINC:LA6675-8 | Benign +LOINC:LA4489-6 | Unknown +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.component:Variant.Interpretation +- GA4GH Phenopacket Schema v2.0 Element: Interpretation.AcmgPathogenicityClassification" +ga4gh_therap_action,rarelink_6_1_genetic_findings,,dropdown,6.1.15 Therapeutic Actionability,"ga4gh_unknown_actionability, There is not enough information at this time to support any therapeutic actionability for this variant | ga4gh_not_actionable, This variant has no therapeutic actionability. | ga4gh_actionable, This variant is known to be therapeutically actionable.","An enumeration flagging the variant as being a candidate for treatment/ clinical intervention of the disorder caused by this variant, which could improve the clinical outcome.",,,,,,,,,,,"Variable: +GA4GH:therapeutic_actionability | Therapeutic Actionability +Choices: +GA4GH:UNKNOWN_ACTIONABILITY | There is not enough information at this time to support any therapeutic actionability for this variant +GA4GH:NOT_ACTIONABLE | This variant has no therapeutic actionability. +GA4GH:ACTIONABLE | This variant is known to be therapeutically actionable. +Version(s): +- GA4GH Phenopacket Schema Version 2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: [...].GenomicInterpretation.VariantInterpretation.therapeutic_actionability" +loinc_93044_6,rarelink_6_1_genetic_findings,,dropdown,6.1.16 Clinical Annotation Level Of Evidence,"loinc_la30200-2, Very strong evidence pathogenic | loinc_la30201-0, Strong evidence pathogenic | loinc_la30202-8, Moderate evidence pathogenic | loinc_la30203-6, Supporting evidence pathogenic | loinc_la30204-4, Supporting evidence benign | loinc_la30205-1, Strong evidence benign | loinc_la30206-9, Stand-alone evidence pathogenic",The level of evidence supporting the clinical annotation of the genetic variant.,,,,,,,,,,,"Variable: +LOINC:93044-6 | Clinical Annotation Level Of Evidence +Choices: +LOINC:LA30200-2 | Very strong evidence pathogenic +LOINC:LA30201-0 | Strong evidence pathogenic +LOINC:LA30202-8 | Moderate evidence pathogenic +LOINC:LA30203-6 | Supporting evidence pathogenic +LOINC:LA30204-4 | Supporting evidence benign +LOINC:LA30205-1 | Strong evidence benign +LOINC:LA30206-9 | Stand-alone evidence pathogenic +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.extension:Variant.Interpretation +- GA4GH Phenopacket Schema v2.0 Elemen: n/a" +phenotypic_feature_descr,rarelink_6_2_phenotypic_feature,RareLink - 6.2) Phenotypic Findings,descriptive,"
+

Notes for entering information into the Phenotypic Feature sheet

+ +
",,,,,,,,,,,,, +snomed_8116006,rarelink_6_2_phenotypic_feature,,text,6.2.1 Phenotypic Feature,BIOPORTAL:HP,An observed physical and clinical characteristic encoded with HPO.,,,,,,,,,,,"Variable: +SNOMED:8116006 | Phenotypic Feature +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.Code +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.type" +snomed_8116006_date,rarelink_6_2_phenotypic_feature,,text,6.2.2 Determination Date,,"The date on which the phenotypic feature was observed or recorded (we the time it was observed). If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively",date_ymd,,,,,,,,,,"Variable: +SNOMED:439272007:704321009=363778006 | Determination Date +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.effectiveDateTime +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.onset " +ga4gh_pheno_excluded,rarelink_6_2_phenotypic_feature,,dropdown,6.2.3 Status,"snomed_410605003, Confirmed present | snomed_723511001, Refuted","The current status of the phenotypic feature, indicating whether it is confirmed or refuted.",,,,,,,,,,,"Variable: +GA4GH:phenotypicfeature.excluded | Status +Choices: +- SNOMED:410605003 | Confirmed present +- SNOMED:723511001 | Refuted +Version(s): +- GA4GH Phenopacket Schema v2.0 +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Observation.Status (Rec VS: observation.status) +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.excluded " +ga4gh_pheno_mod_hp1,rarelink_6_2_phenotypic_feature,,text,6.2.4 Clinical Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers to describe a specific phenotypic feature, if possible part of these: https://hpo.jax.org/browse/term/HP:0012823 ",,,,,,,,,,,"Variable: +GA4GH:phenotypicfeature.modifier | Modifier +Choices: +n/a +Version(s): +- GA4GH Phenopacket Schema v2.0 +Mapping: +- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" +ga4gh_pheno_mod_hp2,rarelink_6_2_phenotypic_feature,,text,6.2.4 Clinical Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers to describe a specific phenotypic feature, if possible part of these: https://hpo.jax.org/browse/term/HP:0012823 ",,,,,"[ga4gh_pheno_mod_hp1] <> """"",,,,,,"Variable: +GA4GH:phenotypicfeature.modifier | Modifier +Choices: +n/a +Version(s): +- GA4GH Phenopacket Schema v2.0 +Mapping: +- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" +ga4gh_pheno_mod_hp3,rarelink_6_2_phenotypic_feature,,text,6.2.4 Clinical Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers to describe a specific phenotypic feature, if possible part of these: https://hpo.jax.org/browse/term/HP:0012823 ",,,,,"[ga4gh_pheno_mod_hp2] <> """"",,,,,,"Variable: +GA4GH:phenotypicfeature.modifier | Modifier +Choices: +n/a +Version(s): +- GA4GH Phenopacket Schema v2.0 +Mapping: +- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" +ga4gh_pheno_mod_ncbitax,rarelink_6_2_phenotypic_feature,,text,"6.2.4 If applicable, what was the causing organism? [NCBITAXON]",BIOPORTAL:NCBITAXON,"If applicable, select the causing organism. To search more easily, consider searching in https://www.ebi.ac.uk/ols4/ontologies. It is recommended to select a common set of choices if capturing phenotypes for a cohort. ",,,,,,,,,,,"Variable: +GA4GH:phenotypicfeature.modifier | Modifier +Choices: +n/a +Version(s): +- GA4GH Phenopacket Schema v2.0 +Mapping: +- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" +ga4gh_pheno_mod_snomed,rarelink_6_2_phenotypic_feature,,text,"6.2.4I If applicable, what was the primary body site? [SNOMED]",BIOPORTAL:SNOMEDCT,"If applicable, select the primary bodysite. To search more easily, consider searching in https://www.ebi.ac.uk/ols4/ontologies. It is recommended to select a common set of choices if capturing phenotypes for a cohort.",,,,,,,,,,,"Variable: +GA4GH:phenotypicfeature.modifier | Modifier +Choices: +n/a +Version(s): +- GA4GH Phenopacket Schema v2.0 +Mapping: +- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension +- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" +family_history_descr,rarelink_6_3_family_history,RareLink - 6.3) Family History,descriptive,"
+

Notes for entering information into the Family History sheet

+ +
",,,,,,,,,,,,, +family_history_pseudonym,rarelink_6_3_family_history,,text,6.3.0 Pseudonym,,"If a pseudonym was already assigned to the specific family member, please enter it here to identify across records.",,,,,,,,,,, +snomed_64245008,rarelink_6_3_family_history,,dropdown,6.3.1 Propositus/-a,"snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown | snomed_1220561009, Not recorded","Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members.",,,,,,,,,,,"SNOMED:64245008 | Propositus/-a +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives → 1 Phenopacket per family member) " +snomed_408732007,rarelink_6_3_family_history,,dropdown,6.3.2 Relationship of the individual to the index case / propositus/a,"snomed_65656005, Natural mother | snomed_9947008, Natural father | snomed_83420006, Natural daughter | snomed_113160008, Natural son | snomed_60614009, Natural brother | snomed_73678001, Natural sister | snomed_11286003, Twin sibling | snomed_45929001, Half-brother | snomed_2272004, Half-sister | snomed_62296006, Natural grandfather | snomed_17945006, Natural grandmother | snomed_1220561009, Not recorded","Specifies the familial relationship of the individual being evaluated to the index case or propositus/proposita. +Disclaimer:",,,,,,,,,,,"SNOMED:408732007 | Relationship of the individual to the index case / propositus/a +Choices: +- SNOMED:65656005 | Natural mother +- SNOMED:9947008 | Natural father +- SNOMED:83420006 | Natural daughter +- SNOMED:113160008 | Natural son +- SNOMED:60614009 | Natural brother +- SNOMED:73678001 | Natural sister +- SNOMED:11286003 | Twin sibling +- SNOMED:45929001 | Half-brother +- SNOMED:2272004 | Half-sister +- SNOMED:62296006 | Natural grandfather +- SNOMED:17945006 | Natural grandmother +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives → 1 Phenopacket per family member) " +snomed_842009,rarelink_6_3_family_history,,dropdown,6.3.3 Consanguinity,"snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown | snomed_1220561009, Not recorded","The presence of a biological relationship between parents who are related by blood, typically as first or second cousins.",,,,,,,,,,,"Variable: +SNOMED:842009 | Consanguinity +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Family.consanguinous_parents +- GA4GH Phenopacket Schema v2.0 Element: (Family.consanguinous_parents) " +snomed_444018008,rarelink_6_3_family_history,,dropdown,6.3.4 Family Member Relationship,"snomed_65656005, Natural mother | snomed_9947008, Natural father | snomed_83420006, Natural daughter | snomed_113160008, Natural son | snomed_60614009, Natural brother | snomed_73678001, Natural sister | snomed_11286003, Twin sibling | snomed_45929001, Half-brother | snomed_2272004, Half-sister | snomed_62296006, Natural grandfather | snomed_17945006, Natural grandmother | snomed_1220561009, Not recorded",Specifies the relationship of the selected family member to the patient.,,,,,,,,,,,"Variable: +SNOMED:444018008 | Family Member Relationship +Choices: +- SNOMED:65656005 | Natural mother +- SNOMED:9947008 | Natural father +- SNOMED:83420006 | Natural daughter +- SNOMED:113160008 | Natural son +- SNOMED:60614009 | Natural brother +- SNOMED:73678001 | Natural sister +- SNOMED:11286003 | Twin sibling +- SNOMED:45929001 | Half-brother +- SNOMED:2272004 | Half-sister +- SNOMED:62296006 | Natural grandfather +- SNOMED:17945006 | Natural grandmother +- SNOMED:1220561009 | Not recorded +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.relationship.coding (VS: FamilyMember) +- GA4GH Phenopacket Schema v2.0 Element: Family.Pedigree.Person.individual_id " +hl7fhir_fmh_status,rarelink_6_3_family_history,,dropdown,6.3.5 Family Member Record Status,"hl7fhir_partial, Partial | hl7fhir_completed, Completed | hl7fhir_entered-in-error, Entered in Error | hl7fhir_health-unknown, Health Unknown",Specifies the record’s status of the family history of a specific family member.,,,,,,,,,,,"Variable: +HL7 FHIR:familymemberhistory.status | Family Member Record Status +Choices: +- HL7 FHIR:partial | Partial +- HL7 FHIR:completed | Completed +- HL7 FHIR:entered-in-error | Entered in Error +- HL7 FHIR:health-unknown | Health Unknown +Version(s): +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.status (VS: FamilyHistoryStatus) +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +loinc_54123_5,rarelink_6_3_family_history,,dropdown,6.3.6 Family Member Sex,"snomed_248152002, Female | snomed_248153007, Male | snomed_184115007, Patient sex unknown | snomed_32570691000036108, Intersex | snomed_1220561009, Not recorded","Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected.",,,,,,,,,,,"Variable: +LOINC:54123-5 | Family Member Sex +Choices: +- SNOMED:248152002 | Female +- SNOMED:248153007 | Male +- SNOMED:184115007 | Patient sex unknown +- SNOMED:32570691000036108 | Intersex +- SNOMED:1220561009 | Not recorded +Version(s): +- LOINC Version 2.77 +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.sex (VS: AdministrativeGender) +- GA4GH Phenopacket Schema v2.0 Element: Family.Pedigree.Person.sex " +loinc_54141_7,rarelink_6_3_family_history,,text,6.3.7 Family Member Age,,Records the current age in full years of the selected family member.,integer,0,200,,,,,,,,"Variable: +LOINC:54141-7 | Family Member Age +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.ageAge +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +loinc_54124_3,rarelink_6_3_family_history,,text,6.3.8 Family Member Date of Birth,,Records the date of birth of the selected family member.,date_ymd,,,,,,,,,,"Variable: +LOINC:54124-3 | Family Member Date of Birth +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.bornDate +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +snomed_740604001,rarelink_6_3_family_history,,dropdown,6.3.9 Family Member Deceased,"snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown",Indicates whether the selected family member is deceased.,,,,,,,,,,,"Variable: +SNOMED:740604001 | Family Member Deceased +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.deceased.deceasedBoolean +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +loinc_54112_8,rarelink_6_3_family_history,,text,6.3.10 Family Member Cause of Death [ICD10CM],BIOPORTAL:ICD10CM,Records the cause of death of the selected deceased family member.,,,,,[snomed_740604001] = 'snomed_373066001',,,,,,"Variable: +LOINC:54112-8 | Family Member Cause of Death +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +loinc_92662_6,rarelink_6_3_family_history,,text,6.3.11 Family Member Deceased Age,,Records the current age in full years of the selected family member. ,integer,0,200,,[snomed_740604001] = 'snomed_373066001',,,,,,"Variable: +LOINC:92662-6 | Family Member Deceased Age +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.deceasedAge +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +loinc_75315_2,rarelink_6_3_family_history,,text,6.3.12 Family Member Disease [MONDO],BIOPORTAL:MONDO,Indicates whether the selected family member is affected by the same RD as the individual or a different rare disease.,,,,,,,,,,,"Variable: +LOINC:75315-2 | Family Member Disease +Choices: +n/a +Version(s): +- LOINC Version 2.77 +Mapping: +- HL7 FHIR Expression v4.0.1: FamilyMemberHistory.condition.code +- GA4GH Phenopacket Schema v2.0 Element: (Family.relatives) " +consent_descr,rarelink_7_consent,RareLink - 7) Consent,descriptive,"
+

Notes for entering information into the Consent sheet

+ +
+",,,,,,,,,,,,, +snomed_309370004,rarelink_7_consent,,dropdown,7.1 Consent Status,"hl7fhir_draft, Pending | hl7fhir_proposed, Proposed | hl7fhir_active, Active | hl7fhir_rejected, Rejected | hl7fhir_inactive, Inactive | hl7fhir_entered-in-error, Entered in Error",Indicates the current status of the consent.,,,,,,,,,,,"Variable: +SNOMED:309370004 | Consent Status +Choices: +- HL7FHIR:draft | Pending +- HL7FHIR:proposed | Proposed +- HL7FHIR:active | Active +- HL7FHIR:rejected | Rejected +- HL7FHIR:inactive | Inactive +- HL7FHIR:entered-in-error | Entered in Error +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Consent.status +- GA4GH Phenopacket Schema v2.0 Element: n/a " +hl7fhir_consent_datetime,rarelink_7_consent,,text,7.2 Consent Date,,Records the date when the consent was given.,date_ymd,,,,,,,,,,"Variable: +HL7 FHIR:consent.datetime | Consent Date +Choices: +n/a +Version(s): +- HL7 FHIR Version 4.0.1 +Mapping: +- HL7 FHIR Expression v4.0.1: Consent.dateTime +- GA4GH Phenopacket Schema v2.0 Element: n/a " +snomed_386318002,rarelink_7_consent,,text,7.3 Health Policy Monitoring,,"The references to the policies that are included in this consent scope. Policies may be organisational, but are often defined jurisdictionally, or in law.",,,,,,,,,,,"Variable: +SNOMED:386318002 | Health Policy Monitoring +Choices: +n/a +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Consent.policy +- GA4GH Phenopacket Schema v2.0 Element: n/a " +rarelink_consent_contact,rarelink_7_consent,,dropdown,"7.4 Agreement to be +contacted for +research purposes","snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown +",Indicates whether the patient agrees to be contacted for research purposes.,,,,,,,,,,,"Variable: +RareLinkCode:consent_contact_research | Agreement to be contacted for research purposes +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +Version(s): +- RareLink Custom Codes Version 2.0 +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Consent.scope.coding +- GA4GH Phenopacket Schema v2.0 Element: n/a " +rarelink_consent_data,rarelink_7_consent,,dropdown,"7.5 Consent to the reuse +of data","snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown +",Indicates whether the patient consents to the reuse of their data.,,,,,,,,,,,"Variable: +RareLinkCode:conset_data_reuse | Consent to the reuse of data +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +Version(s): +- RareLink Custom Codes Version 2.0 +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: Consent.scope.coding +- GA4GH Phenopacket Schema v2.0 Element: n/a " +snomed_123038009,rarelink_7_consent,,dropdown,7.6 Biological sample,"snomed_373066001, Yes | snomed_373067005, No | snomed_261665006, Unknown +",Indicates whether a patient's biological sample is available for research.,,,,,,,,,,,"Variable: +SNOMED:123038009 | Biological sample +Choices: +- SNOMED:373066001 | Yes +- SNOMED:373067005 | No +- SNOMED:261665006 | Unknown +Version(s): +- SNOMED CT Version 23.2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: n/a " +rarelink_biobank_link,rarelink_7_consent,,text,7.7 Link to a biobank,,"If there is a biological sample, this data element indicates the link to the biobank of the patient's biological sample.",,,,,,,,,,,"Variable: +RareLinkCode:biobank_link | Link to a biobank +Choices: +n/a +Version(s): +- RareLink Custom Codes Version 2.0 +Mapping: +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: n/a " +disability_descr,rarelink_8_disability,RareLink - 8) Disability,descriptive,"
+

Notes for entering information into the Disability sheet

+ +
",,,,,,,,,,,,, +rarelink_icf_score,rarelink_8_disability,,text,8.1 Classification of functioning / disability,BIOPORTAL:ICF,,,,,,,,,,,,"Variable: +RareLinkCode:icf_score | Classification of functioning / disability +Choices: +n/a +Version(s): +- RareLink Custom Codes Version 2.0 +Mapping: +- ICF: Classification of functioning / disability +- HL7 FHIR Expression v4.0.1: n/a +- GA4GH Phenopacket Schema v2.0 Element: n/a" \ No newline at end of file diff --git a/submodules/phenopacket_mapper b/submodules/phenopacket_mapper index 9428601b..321dbfa3 160000 --- a/submodules/phenopacket_mapper +++ b/submodules/phenopacket_mapper @@ -1 +1 @@ -Subproject commit 9428601b907d3593b89996fb8240335fac042fdd +Subproject commit 321dbfa3351a5ecccb7e973c5cdb1c92a7471a8c