diff --git a/res/RareLink2.0_Test_Data.csv b/res/RareLink2.0_Test_Data.csv deleted file mode 100644 index 53731b0d..00000000 --- a/res/RareLink2.0_Test_Data.csv +++ /dev/null @@ -1,74 +0,0 @@ -record_id,redcap_repeat_instrument,redcap_repeat_instance,redcap_survey_identifier,rarelink_1_formal_criteria_timestamp,snomed_422549004,snomed_399423000,rarelink_1_formal_criteria_complete,snomed_184099003,snomed_281053000,snomed_1296886006,snomed_263495000,snomed_370159000,rarelink_2_personal_information_complete,patient_status_date,snomed_278844005,snomed_398299004,snomed_184305005,snomed_105727008,snomed_412726003,snomed_723663001,rarelink_3_patient_status_complete,hl7fhir_enc_period_start,hl7fhir_enc_period_end,snomed_305058001,hl7fhir_encounter_class,rarelink_4_care_pathway_complete,snomed_64572001_mondo,snomed_64572001_ordo,snomed_64572001_icd10cm,snomed_64572001_icd11,snomed_64572001_omim_p,loinc_99498_8,snomed_424850005,snomed_298059007,snomed_423493009,snomed_432213005,snomed_363698007,snomed_263493007,snomed_246112005,rarelink_5_disease_complete,snomed_106221001_mondo,snomed_106221001_omim_p,ga4gh_progress_status,ga4gh_interp_status,loinc_81304_8,loinc_62374_4,loinc_lp7824_8,loinc_81290_9,loinc_48004_6,loinc_48005_3,loinc_48018_6,loinc_48018_6_label,loinc_53034_5,loinc_53034_5_other,loinc_48002_0,loinc_48019_4,loinc_48019_4_other,loinc_53037_8,ga4gh_therap_action,loinc_93044_6,rarelink_6_1_genetic_findings_complete,snomed_8116006,snomed_8116006_date,ga4gh_pheno_excluded,ga4gh_pheno_mod_hp1,ga4gh_pheno_mod_hp2,ga4gh_pheno_mod_hp3,ga4gh_pheno_mod_ncbitax1,ga4gh_pheno_mod_ncbitax2,ga4gh_pheno_mod_ncbitax3,ga4gh_pheno_mod_snomed1,ga4gh_pheno_mod_snomed2,ga4gh_pheno_mod_snomed3,rarelink_6_2_phenotypic_feature_complete,family_history_pseudonym,snomed_64245008,snomed_408732007,snomed_842009,snomed_444018008,hl7fhir_fmh_status,loinc_54123_5,loinc_54141_7,loinc_54124_3,snomed_740604001,loinc_54112_8,loinc_92662_6,loinc_75315_2,rarelink_6_3_family_history_complete,snomed_309370004,hl7fhir_consent_datetime,snomed_386318002,rarelink_consent_contact,rarelink_consent_data,snomed_123038009,rarelink_biobank_link,rarelink_7_consent_complete,rarelink_icf_score,rarelink_8_disability_complete -1,,,,,ABC123,2023-12-23,,2016-12-21,snomed_248152002,nomed_734875008,snomed_1220561009,GER,,,,,,,,,,2007-04-15,2017-01-16,hl7fhir_in-progress,hl7fhir_obsenc,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_rejected,2004-03-19,random_string,snomed_373066001,snomed_373067005,snomed_261665006,random_string,,random_string, -1,rarelink_3_patient_status,1,,,,,,,,,,,,2020-01-22,snomed_438949009,,,snomed_255398004,,35+5,snomed_373067005,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_3_patient_status,2,,,,,,,,,,,,2023-06-06,snomed_419099009,2023-05-01,ICD10CM:R56.01,,,,snomed_373067005,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2020-01-15,2020-01-25,hl7fhir_finished,hl7fhir_imp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2022-03-09,2022-04-28,hl7fhir_finished,hl7fhir_imp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,,,,hl7fhir_confirmed,snomed_3950001,,snomed_3950001,2016-12-21,,hl7fhir_active,snomed_24484000,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0958229,,,,,hl7fhir_differential,snomed_410672004,2020-01-02,snomed_410672004,2020-01-19,SNOMED:8157004,hl7fhir_remission,snomed_6736007,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0012242,,,,,hl7fhir_confirmed,snomed_410672004,2022-03-02,snomed_410672004,2022-03-14,,hl7fhir_resolved,snomed_24484000,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,ga4gh_in_progress,ga4gh_rejected,loinc_la26813-8,loinc_la14031-1,,,NM_024420.3:c.15T>C,,HGNC:9035,PLA2G4A,loinc_la6706-1,,loinc_la26807-0,loinc_la9658-1,,loinc_la26333-7,ga4gh_unknown_actionability,loinc_la30203-6,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,ga4gh_unsolved,ga4gh_contributory,loinc_la26406-1,loinc_la14031-1,,,NM_024420.3:c.687C>G,,HGNC:9035,PLA2G4A,loinc_la6703-8,,loinc_la18195-0,loinc_la6690-7,,loinc_la26333-7,ga4gh_not_actionable,loinc_la30202-8,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,OMIM:187900,ga4gh_unknown_progress,ga4gh_unknown_status,loinc_la26810-4,loinc_la14030-3,,,NM_001377304.1:c.-16G>A,,HGNC:4238,GFI1B,loinc_la6705-3,,loinc_la26807-0,loinc_48019_4_other,,loinc_la4489-6,ga4gh_unknown_actionability,loinc_la30200-2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001892,2020-01-07,snomed_410605003,HP:0012828,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001279,2022-05-02,snomed_410605003,HP:0012828,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0100806,2023-08-28,snomed_410605003,HP:0012826,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001287,2022-06-02,snomed_410605003,HP:0012826,,,85279,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_3_family_member_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ZUO789,snomed_373066001,snomed_113160008,snomed_373067005,snomed_11286003,hl7fhir_health-unknown,snomed_32570691000036108,random_string,2015-05-12,snomed_261665006,,,,,,,,,,,,,, -1,rarelink_6_3_family_member_history,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,POI293,snomed_1220561009,snomed_45929001,snomed_373067005,snomed_9947008,hl7fhir_partial,snomed_248153007,random_string,2017-05-22,snomed_373067005,,,,,,,,,,,,,, -1,rarelink_6_3_family_member_history,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,NJK482,snomed_1220561009,snomed_2272004,snomed_1220561009,snomed_113160008,hl7fhir_partial,snomed_32570691000036108,random_string,2023-10-21,snomed_373066001,,,,,,,,,,,,,, -45,,,,,BCD234,2024-09-09,2,2022-09-07,snomed_248153007,snomed_734876009,snomed_446151000124109,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_active,2024-01-09,,,,,,0,,0 -45,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_3658006,33+6,snomed_373067005,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-19,hl7fhir_finished,hl7fhir_imp,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2023-01-09,2023-01-22,hl7fhir_finished,hl7fhir_imp,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0600019,,,,,hl7fhir_confirmed,snomed_410672004,2023-01-02,snomed_410672004,2023-05-09,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0957580,,,,,hl7fhir_differential,snomed_410672004,2024-07-09,,,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0005851,,,,,hl7fhir_refuted,,,,,,hl7fhir_resolved,,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0600019,,ga4gh_completed,ga4gh_causative,loinc_la26418-6,loinc_la26806-2,,NC_000017.11:g.61455901C>G,,,HGNC:11603,TBX4,loinc_la6706-1,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30203-6,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0957580,,ga4gh_unsolved,ga4gh_rejected,loinc_la26404-6,loinc_la26806-2,,,NM_001145160.2:c.59A>T,,HGNC:12013,TPM4,loinc_la6706-1,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30202-8,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0032892,2023-09-09,snomed_410605003,HP:0031796,HP:0012828,,85278,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000252,2023-01-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001892,2022-09-09,snomed_410605003,HP:0031796,HP:0012825,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001287,2023-09-09,snomed_723511001,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,WOF425,snomed_373067005,,snomed_373067005,snomed_9947008,hl7fhir_partial,snomed_248153007,55,1974-09-09,snomed_373067005,,,,0,,,,,,,,,, -45,rarelink_6_3_family_history,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,WGP592,snomed_373066001,snomed_60614009,snomed_373067005,snomed_73678001,hl7fhir_completed,snomed_248152002,7,2017-09-09,snomed_373066001,S09.90,,MONDO:0957580,0,,,,,,,,,, -46,,,,,CDE456,2024-09-09,0,2020-01-01,snomed_248152002,snomed_80427008,snomed_446141000124107,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_proposed,,,,,snomed_261665006,,1,,2 -46,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_255398004,36+5,snomed_373067005,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-29,hl7fhir_finished,hl7fhir_imp,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0021163,,,,,hl7fhir_confirmed,,,,2023-09-10,,hl7fhir_resolved,snomed_6736007,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0019499,ORPHA:881,Q96,,,hl7fhir_confirmed,snomed_3950001,,snomed_410672004,2020-01-28,,hl7fhir_active,snomed_6736007,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0002078,,,,,hl7fhir_confirmed,snomed_410672004,2020-05-09,snomed_410672004,2020-09-09,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,4,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0002367,,,,,hl7fhir_provisional,,,snomed_410672004,2024-09-01,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0019499,,ga4gh_completed,ga4gh_candidate,loinc_la26404-6,loinc_la26806-2,,,NM_024420.3:c.15T>C,,HGNC:10853,SHOX,loinc_la6706-1,,loinc_la10429-1,loinc_la6686-5,,loinc_la26333-7,ga4gh_not_actionable,loinc_la30201-0,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001059,2020-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002967,2020-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002665,2021-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0004322,2020-09-09,snomed_410605003,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,OTI398,snomed_373066001,,snomed_373067005,snomed_45929001,hl7fhir_partial,snomed_248153007,,2021-09-09,snomed_261665006,,,,2,,,,,,,,,, -47,,,,,DEF567,2024-09-09,2,2010-01-01,snomed_248152002,snomed_65162001,snomed_446141000124107,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_active,2023-09-09,,,,snomed_373067005,,2,,2 -47,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_263659003,37+1,snomed_373067005,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2022-09-09,,hl7fhir_in-progress,hl7fhir_amb,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-30,hl7fhir_finished,hl7fhir_imp,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0006823,ORPHA:484,Q98.0,,,hl7fhir_confirmed,snomed_410672004,2014-09-09,snomed_410672004,2014-09-30,,hl7fhir_active,snomed_6736007,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0006823,,ga4gh_in_progress,ga4gh_rejected,loinc_la26418-6,loinc_la26806-2,,,NM_001377304.1:c.-16G>A,,,,loinc_la6705-3,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30201-0,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000866,2020-09-09,snomed_410605003,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000133,2022-09-09,snomed_410605003,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000823,2022-09-09,snomed_410605003,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,GOW204,snomed_373066001,,snomed_373066001,snomed_65656005,,snomed_248152002,44,1980-09-09,snomed_373067005,,,MONDO:0006823,2,,,,,,,,,, -48,,,,,EFG678,2024-09-09,2,2020-01-01,snomed_248153007,snomed_734876009,snomed_1220561009,TUR,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_active,2024-03-09,,,,snomed_373067005,,2,,2 -48,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_713153009,37+3,snomed_373066001,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2021-09-09,2021-09-30,hl7fhir_finished,hl7fhir_imp,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2021-09-09,,hl7fhir_in-progress,hl7fhir_amb,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0010518,ORPHA:906,,,,hl7fhir_differential,snomed_410672004,2021-08-09,,,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0021679,,,,,hl7fhir_confirmed,,2021-05-09,,2021-09-12,,hl7fhir_recurrence,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0010518,301000,ga4gh_unsolved,ga4gh_candidate,loinc_la26404-6,loinc_la26806-2,,NC_000023.11:g.48683512T>C,,,HGNC:12731,WAS,loinc_la6706-1,,loinc_la18194-3,loinc_la6692-3,,loinc_la26332-9,ga4gh_actionable,loinc_la30200-2,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0010518,301000,ga4gh_in_progress,ga4gh_contributory,loinc_la26418-6,loinc_la26806-2,,,NM_000377.3:c.6T>C,,,,loinc_la6705-3,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30201-0,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002719,2023-09-09,snomed_410605003,HP:0012828,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000979,2023-09-09,snomed_410605003,HP:0012825,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0011127,2023-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0012059,2023-09-09,snomed_723511001,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,GLW409,snomed_373067005,,snomed_373067005,snomed_60614009,hl7fhir_partial,snomed_248152002,11,2013-09-09,snomed_373067005,,,,1,,,,,,,,,, \ No newline at end of file diff --git a/res/RareLink2.0_Test_Data_no_family.csv b/res/RareLink2.0_Test_Data_no_family.csv deleted file mode 100644 index 74f33596..00000000 --- a/res/RareLink2.0_Test_Data_no_family.csv +++ /dev/null @@ -1,65 +0,0 @@ -record_id,redcap_repeat_instrument,redcap_repeat_instance,redcap_survey_identifier,rarelink_1_formal_criteria_timestamp,snomed_422549004,snomed_399423000,rarelink_1_formal_criteria_complete,snomed_184099003,snomed_281053000,snomed_1296886006,snomed_263495000,snomed_370159000,rarelink_2_personal_information_complete,patient_status_date,snomed_278844005,snomed_398299004,snomed_184305005,snomed_105727008,snomed_412726003,snomed_723663001,rarelink_3_patient_status_complete,hl7fhir_enc_period_start,hl7fhir_enc_period_end,snomed_305058001,hl7fhir_encounter_class,rarelink_4_care_pathway_complete,snomed_64572001_mondo,snomed_64572001_ordo,snomed_64572001_icd10cm,snomed_64572001_icd11,snomed_64572001_omim_p,loinc_99498_8,snomed_424850005,snomed_298059007,snomed_423493009,snomed_432213005,snomed_363698007,snomed_263493007,snomed_246112005,rarelink_5_disease_complete,snomed_106221001_mondo,snomed_106221001_omim_p,ga4gh_progress_status,ga4gh_interp_status,loinc_81304_8,loinc_62374_4,loinc_lp7824_8,loinc_81290_9,loinc_48004_6,loinc_48005_3,loinc_48018_6,loinc_48018_6_label,loinc_53034_5,loinc_53034_5_other,loinc_48002_0,loinc_48019_4,loinc_48019_4_other,loinc_53037_8,ga4gh_therap_action,loinc_93044_6,rarelink_6_1_genetic_findings_complete,snomed_8116006,snomed_8116006_date,ga4gh_pheno_excluded,ga4gh_pheno_mod_hp1,ga4gh_pheno_mod_hp2,ga4gh_pheno_mod_hp3,ga4gh_pheno_mod_ncbitax1,ga4gh_pheno_mod_ncbitax2,ga4gh_pheno_mod_ncbitax3,ga4gh_pheno_mod_snomed1,ga4gh_pheno_mod_snomed2,ga4gh_pheno_mod_snomed3,rarelink_6_2_phenotypic_feature_complete,family_history_pseudonym,snomed_64245008,snomed_408732007,snomed_842009,snomed_444018008,hl7fhir_fmh_status,loinc_54123_5,loinc_54141_7,loinc_54124_3,snomed_740604001,loinc_54112_8,loinc_92662_6,loinc_75315_2,rarelink_6_3_family_history_complete,snomed_309370004,hl7fhir_consent_datetime,snomed_386318002,rarelink_consent_contact,rarelink_consent_data,snomed_123038009,rarelink_biobank_link,rarelink_7_consent_complete,rarelink_icf_score,rarelink_8_disability_complete -1,,,,,ABC123,2023-12-23,,2016-12-21,snomed_248152002,nomed_734875008,snomed_1220561009,GER,,,,,,,,,,2007-04-15,2017-01-16,hl7fhir_in-progress,hl7fhir_obsenc,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_rejected,2004-03-19,random_string,snomed_373066001,snomed_373067005,snomed_261665006,random_string,,random_string, -1,rarelink_3_patient_status,1,,,,,,,,,,,,2020-01-22,snomed_438949009,,,snomed_255398004,,35+5,snomed_373067005,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_3_patient_status,2,,,,,,,,,,,,2023-06-06,snomed_419099009,2023-05-01,ICD10CM:R56.01,,,,snomed_373067005,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2020-01-15,2020-01-25,hl7fhir_finished,hl7fhir_imp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2022-03-09,2022-04-28,hl7fhir_finished,hl7fhir_imp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,,,,hl7fhir_confirmed,snomed_3950001,,snomed_3950001,2016-12-21,,hl7fhir_active,snomed_24484000,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0958229,,,,,hl7fhir_differential,snomed_410672004,2020-01-02,snomed_410672004,2020-01-19,SNOMED:8157004,hl7fhir_remission,snomed_6736007,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0012242,,,,,hl7fhir_confirmed,snomed_410672004,2022-03-02,snomed_410672004,2022-03-14,,hl7fhir_resolved,snomed_24484000,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,ga4gh_in_progress,ga4gh_rejected,loinc_la26813-8,loinc_la14031-1,,,NM_024420.3:c.15T>C,,HGNC:9035,PLA2G4A,loinc_la6706-1,,loinc_la26807-0,loinc_la9658-1,,loinc_la26333-7,ga4gh_unknown_actionability,loinc_la30203-6,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0018794,,ga4gh_unsolved,ga4gh_contributory,loinc_la26406-1,loinc_la14031-1,,,NM_024420.3:c.687C>G,,HGNC:9035,PLA2G4A,loinc_la6703-8,,loinc_la18195-0,loinc_la6690-7,,loinc_la26333-7,ga4gh_not_actionable,loinc_la30202-8,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_1_genetic_findings,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,OMIM:187900,ga4gh_unknown_progress,ga4gh_unknown_status,loinc_la26810-4,loinc_la14030-3,,,NM_001377304.1:c.-16G>A,,HGNC:4238,GFI1B,loinc_la6705-3,,loinc_la26807-0,loinc_48019_4_other,,loinc_la4489-6,ga4gh_unknown_actionability,loinc_la30200-2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001892,2020-01-07,snomed_410605003,HP:0012828,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001279,2022-05-02,snomed_410605003,HP:0012828,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -1,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0100806,2023-08-28,snomed_410605003,HP:0012826,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,,,,,BCD234,2024-09-09,2,2022-09-07,snomed_248153007,snomed_734876009,snomed_446151000124109,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_active,2024-01-09,,,,,,0,,0 -45,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_3658006,33+6,snomed_373067005,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-19,hl7fhir_finished,hl7fhir_imp,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2023-01-09,2023-01-22,hl7fhir_finished,hl7fhir_imp,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0600019,,,,,hl7fhir_confirmed,snomed_410672004,2023-01-02,snomed_410672004,2023-05-09,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0957580,,,,,hl7fhir_differential,snomed_410672004,2024-07-09,,,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0005851,,,,,hl7fhir_refuted,,,,,,hl7fhir_resolved,,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0600019,,ga4gh_completed,ga4gh_causative,loinc_la26418-6,loinc_la26806-2,,NC_000017.11:g.61455901C>G,,,HGNC:11603,TBX4,loinc_la6706-1,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30203-6,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0957580,,ga4gh_unsolved,ga4gh_rejected,loinc_la26404-6,loinc_la26806-2,,,NM_001145160.2:c.59A>T,,HGNC:12013,TPM4,loinc_la6706-1,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30202-8,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0032892,2023-09-09,snomed_410605003,HP:0031796,HP:0012828,,85278,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000252,2023-01-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001892,2022-09-09,snomed_410605003,HP:0031796,HP:0012825,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -45,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001287,2023-09-09,snomed_723511001,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,,,,,CDE456,2024-09-09,0,2020-01-01,snomed_248152002,snomed_80427008,snomed_446141000124107,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_proposed,,,,,snomed_261665006,,1,,2 -46,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_255398004,36+5,snomed_373067005,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-29,hl7fhir_finished,hl7fhir_imp,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0021163,,,,,hl7fhir_confirmed,,,,2023-09-10,,hl7fhir_resolved,snomed_6736007,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0019499,ORPHA:881,Q96,,,hl7fhir_confirmed,snomed_3950001,,snomed_410672004,2020-01-28,,hl7fhir_active,snomed_6736007,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0002078,,,,,hl7fhir_confirmed,snomed_410672004,2020-05-09,snomed_410672004,2020-09-09,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_5_disease,4,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0002367,,,,,hl7fhir_provisional,,,snomed_410672004,2024-09-01,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0019499,,ga4gh_completed,ga4gh_candidate,loinc_la26404-6,loinc_la26806-2,,,NM_024420.3:c.15T>C,,HGNC:10853,SHOX,loinc_la6706-1,,loinc_la10429-1,loinc_la6686-5,,loinc_la26333-7,ga4gh_not_actionable,loinc_la30201-0,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001059,2020-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002967,2020-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002665,2021-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -46,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0004322,2020-09-09,snomed_410605003,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -47,,,,,DEF567,2024-09-09,2,2010-01-01,snomed_248152002,snomed_65162001,snomed_446141000124107,GER,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,snomed_active,2023-09-09,,,,snomed_373067005,,2,,2 -47,infectionceientest,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_3_patient_status,1,,,,,,,,,,,,2024-09-09,snomed_438949009,,,snomed_263659003,37+1,snomed_373067005,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -47,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2022-09-09,,hl7fhir_in-progress,hl7fhir_amb,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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-48,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000979,2023-09-09,snomed_410605003,HP:0012825,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0011127,2023-09-09,snomed_410605003,,,,,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, -48,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0012059,2023-09-09,snomed_723511001,,,,,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, \ No newline at end of file diff --git a/res/rarelink_cdm_v2_0_0_test_data.csv b/res/rarelink_cdm_v2_0_0_test_data.csv new file mode 100644 index 00000000..08b92871 --- /dev/null +++ b/res/rarelink_cdm_v2_0_0_test_data.csv @@ -0,0 +1,58 @@ 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+103,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0010518,301000,ga4gh_in_progress,ga4gh_contributory,loinc_la26418-6,loinc_la26806-2,,chgvs,,NM_000377.3:c.6T>C,,,,,loinc_la6705-3,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30201-0,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002719,2023-09-09,snomed_410605003,HP:0012828,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +103,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000979,2023-09-09,snomed_410605003,HP:0012825,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +103,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0011127,2023-09-09,snomed_410605003,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, +103,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0012059,2023-09-09,snomed_723511001,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +103,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,GLW409,snomed_373067005,,snomed_373067005,snomed_60614009,hl7fhir_partial,snomed_248152002,11,2013-09-09,snomed_373067005,,,,1,,,,,,,,,, +104,,,,,EFG678,2024-09-09,2,2020-01-01,snomed_248153007,snomed_734876009,snomed_1220561009,TUR,2,2024-09-09,snomed_438949009,,,snomed_713153009,37+3,snomed_373066001,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,hl7fhir_active,2024-03-09,,,,snomed_373067005,,2,,2 +104,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2021-09-09,2021-09-30,hl7fhir_finished,hl7fhir_imp,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_4_care_pathway,2,,,,,,,,,,,,,,,,,,,,2021-09-09,,hl7fhir_in-progress,hl7fhir_amb,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0010518,,,,,hl7fhir_differential,snomed_410672004,2021-08-09,,,,hl7fhir_active,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,,MONDO:0021679,,,,,hl7fhir_confirmed,,2021-05-09,,2021-09-12,,hl7fhir_recurrence,snomed_24484000,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0010518,301000,ga4gh_unsolved,ga4gh_candidate,loinc_la26404-6,loinc_la26806-2,,ghgvs,NC_000023.11:g.48683512T>C,,,,HGNC:12731,WAS,loinc_la6706-1,,loinc_la18194-3,loinc_la6692-3,,loinc_la26332-9,ga4gh_actionable,loinc_la30200-2,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_1_genetic_findings,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0010518,301000,ga4gh_in_progress,ga4gh_contributory,loinc_la26418-6,loinc_la26806-2,,chgvs,,NM_000377.3:c.6T>C,,,,,loinc_la6705-3,,loinc_la6684-0,loinc_la6692-3,,loinc_la26332-9,ga4gh_not_actionable,loinc_la30201-0,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002719,2023-09-09,snomed_410605003,HP:0012828,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0000979,2023-09-09,snomed_410605003,HP:0012825,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0011127,2023-09-09,snomed_410605003,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0012059,2023-09-09,snomed_723511001,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +104,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,GLW409,snomed_373067005,,snomed_373067005,snomed_60614009,hl7fhir_partial,snomed_248152002,11,2013-09-09,snomed_373067005,,,,1,,,,,,,,,, +105,,,,,CDE456,2024-09-09,0,2020-01-01,snomed_248152002,snomed_80427008,snomed_446141000124107,GER,2,2024-09-09,snomed_438949009,,,snomed_255398004,36+5,snomed_373067005,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,hl7fhir_proposed,,,,,snomed_261665006,,1,,2 +105,rarelink_4_care_pathway,1,,,,,,,,,,,,,,,,,,,,2023-09-09,2023-09-29,hl7fhir_finished,hl7fhir_imp,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_5_disease,1,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0021163,,,,,hl7fhir_confirmed,snomed_3950001,,snomed_118189007,2023-09-10,,hl7fhir_resolved,snomed_6736007,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_5_disease,2,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0019499,,,,,hl7fhir_confirmed,snomed_3950001,,snomed_410672004,2020-01-28,,hl7fhir_active,snomed_6736007,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_5_disease,3,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0002078,,,,,hl7fhir_confirmed,snomed_410672004,2020-05-09,snomed_410672004,2020-09-09,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_5_disease,4,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0002367,,,,,hl7fhir_provisional,,,snomed_410672004,2024-09-01,,hl7fhir_active,snomed_24484000,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_1_genetic_findings,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,mondo,MONDO:0019499,,ga4gh_completed,ga4gh_candidate,loinc_la26404-6,loinc_la26806-2,,chgvs,,NM_006883.2:c.-507G>C,,,HGNC:10853,SHOX,loinc_la6706-1,,loinc_la10429-1,loinc_la6686-5,,loinc_la26333-7,ga4gh_not_actionable,loinc_la30201-0,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_2_phenotypic_feature,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0001059,2020-09-09,snomed_410605003,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_2_phenotypic_feature,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002967,2020-09-09,snomed_410605003,,,,,,0,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_2_phenotypic_feature,3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0002665,2021-09-09,snomed_410605003,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_2_phenotypic_feature,4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HP:0004322,2020-09-09,snomed_410605003,,,,,,2,,,,,,,,,,,,,,,,,,,,,,,, +105,rarelink_6_3_family_history,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,OTI398,snomed_373066001,,snomed_373067005,snomed_45929001,hl7fhir_partial,snomed_248153007,,2021-09-09,snomed_261665006,,,,2,,,,,,,,,, \ No newline at end of file diff --git a/res/rarelink_cdm_v2_0_0_test_data.xlsx b/res/rarelink_cdm_v2_0_0_test_data.xlsx new file mode 100644 index 00000000..c94ebfe6 Binary files /dev/null and b/res/rarelink_cdm_v2_0_0_test_data.xlsx differ diff --git a/res/GenAdipositasALTDemo_CDISC_ODM_2024-09-25_1743.xml b/res/rarelink_cdm_v2_0_0_test_data.xml similarity index 53% rename from res/GenAdipositasALTDemo_CDISC_ODM_2024-09-25_1743.xml rename to res/rarelink_cdm_v2_0_0_test_data.xml index c338a17f..1552e9e9 100644 --- a/res/GenAdipositasALTDemo_CDISC_ODM_2024-09-25_1743.xml +++ b/res/rarelink_cdm_v2_0_0_test_data.xml @@ -1,7 +1,10 @@ - + + + + - + @@ -39,7 +42,7 @@ - + @@ -67,7 +70,7 @@ - + @@ -79,16 +82,16 @@ - + - + - + @@ -114,7 +117,7 @@ - + @@ -135,7 +138,7 @@ - + @@ -166,7 +169,7 @@ - + @@ -192,8 +195,8 @@ - - + + @@ -207,8 +210,8 @@ - - + + @@ -222,8 +225,8 @@ - - + + @@ -237,8 +240,8 @@ - - + + @@ -265,10 +268,10 @@ - + - + @@ -295,7 +298,7 @@ - + @@ -306,7 +309,7 @@ - + @@ -350,10 +353,10 @@ - - + + - + @@ -371,7 +374,7 @@ - + @@ -379,13 +382,13 @@ - + - - + + @@ -407,8 +410,8 @@ - - + + @@ -422,8 +425,8 @@ - - + + @@ -437,8 +440,8 @@ - - + + @@ -465,10 +468,10 @@ - + - + @@ -506,7 +509,7 @@ - + @@ -550,9 +553,9 @@ - + - + @@ -571,7 +574,7 @@ - + @@ -592,7 +595,7 @@ - + @@ -600,7 +603,7 @@ - + @@ -622,7 +625,7 @@ - + @@ -630,7 +633,7 @@ - + @@ -658,8 +661,8 @@ - - + + @@ -673,8 +676,8 @@ - - + + @@ -688,8 +691,8 @@ - - + + @@ -703,8 +706,8 @@ - - + + @@ -730,3 +733,539 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/res/RareLink_CDM_v2.0_DataDictionary.csv b/res/rarelink_v2_0_0_datadictionary.csv similarity index 93% rename from res/RareLink_CDM_v2.0_DataDictionary.csv rename to res/rarelink_v2_0_0_datadictionary.csv index 2e78e69c..f3f18f68 100644 --- a/res/RareLink_CDM_v2.0_DataDictionary.csv +++ b/res/rarelink_v2_0_0_datadictionary.csv @@ -230,7 +230,8 @@ disease_descr,rarelink_5_disease,RareLink - 5) Disease,descriptive,"
If the specific month or day is not known, select the 1st day of the month or the 1st month of the year, respectively (e.g., sometime in June 2022 --> 01.June.2022, sometime in 2014 --> 01.01.2014).
",,,,,,,,,,,,, -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.,,,,,,,,,,,"Variable: +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 @@ -239,7 +240,7 @@ Version(s): 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.,,,,,,,,,,,"Variable: +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 @@ -248,7 +249,7 @@ Version(s): 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.,,,,,,,,,,,"Variable: +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 @@ -257,7 +258,7 @@ Version(s): 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.,,,,,,,,,,,"Variable: +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 @@ -266,7 +267,7 @@ Version(s): 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 respective OMIM_g and OMIM_p codes.",,,,,,,,,,,"Variable: +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 @@ -372,7 +373,7 @@ genetic_findings_descr,rarelink_6_1_genetic_findings,RareLink - 6.1) Genetic Fin ",,,,,,,,,,,,, -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.,,,,,,,,,,,"Variable: +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 @@ -393,7 +395,7 @@ Version(s): 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.,,,,,,,,,,,"Variable: +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 @@ -469,7 +471,8 @@ Version(s): Mapping: - HL7 FHIR Expression v4.0.1: Observation.component:Variant.valueString - GA4GH Phenopacket Schema v2.0 Element: [...].VariantInterpretation.VariationDescriptor.Extension" -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.,,,,,,,,,,,"Variable: +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 @@ -478,7 +481,7 @@ Version(s): 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,,,,,,,,,,,"Variable: +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 @@ -487,7 +490,7 @@ Version(s): 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,,,,,,,,,,,"Variable: +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 @@ -496,6 +499,9 @@ Version(s): 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: @@ -521,7 +527,7 @@ Version(s): 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.,,,,,,,,,,,"Variable: +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 @@ -662,7 +668,7 @@ Version(s): 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 Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers (HP:0012823) to describe a specific phenotypic feature, such as severity.",,,,,,,,,,,"Variable: +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 @@ -671,7 +677,7 @@ Version(s): 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 Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers (HP:0012823) to describe a specific phenotypic feature, such as severity.",,,,,"[ga4gh_pheno_mod_hp1] <> """"",,,,,,"Variable: +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 @@ -680,7 +686,7 @@ Version(s): 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 Modifier [HP],BIOPORTAL:HP,"Further clinical modifiers (HP:0012823) to describe a specific phenotypic feature, such as severity.",,,,,"[ga4gh_pheno_mod_hp2] <> """"",,,,,,"Variable: +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 @@ -689,7 +695,7 @@ Version(s): Mapping: - HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension - GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" -ga4gh_pheno_mod_ncbitax1,rarelink_6_2_phenotypic_feature,,text,6.2.4 Modifier [NCBITAXON],BIOPORTAL:NCBITAXON,Further modifiers encoded with NCBITaxon to link causative infectious agents of a specific phenotypic feature.,,,,,,,,,,,"Variable: +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 @@ -698,43 +704,7 @@ Version(s): Mapping: - HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension - GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier" -ga4gh_pheno_mod_ncbitax2,rarelink_6_2_phenotypic_feature,,text,6.2.4 Modifier [NCBITAXON],BIOPORTAL:NCBITAXON,Further modifiers encoded with NCBITaxon to link causative infectious agents of a specific phenotypic feature.,,,,,"[ga4gh_pheno_mod_ncbitax1] <> """"",,,,,,"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_ncbitax3,rarelink_6_2_phenotypic_feature,,text,6.2.4 Modifier [NCBITAXON],BIOPORTAL:NCBITAXON,Further modifiers encoded with NCBITaxon to link causative infectious agents of a specific phenotypic feature.,,,,,"[ga4gh_pheno_mod_ncbitax2] <> """"",,,,,,"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_snomed1,rarelink_6_2_phenotypic_feature,,text,6.2.4I Modifier [SNOMED],BIOPORTAL:SNOMEDCT,Further modifiers encoded with SNOMED to other clinical characteristics of a specific phenotypic feature.,,,,,,,,,,,"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_snomed2,rarelink_6_2_phenotypic_feature,,text,6.2.4I Modifier [SNOMED],BIOPORTAL:SNOMEDCT,Further modifiers encoded with SNOMED to other clinical characteristics of a specific phenotypic feature.,,,,,"[ga4gh_pheno_mod_snomed1] <> """"",,,,,,"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_snomed3,rarelink_6_2_phenotypic_feature,,text,6.2.4I Modifier [SNOMED],BIOPORTAL:SNOMEDCT,Further modifiers encoded with SNOMED to other clinical characteristics of a specific phenotypic feature.,,,,,"[ga4gh_pheno_mod_snomed2] <> """"",,,,,,"Variable: +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 @@ -905,8 +875,7 @@ consent_descr,rarelink_7_consent,RareLink - 7) Consent,descriptive,"