diff --git a/res/rarelink_cdm_v2_0_0_dev0_datadictionary.csv b/res/rarelink_cdm_v2_0_0_dev0_datadictionary.csv
index 30f0e39f..25b2aafb 100644
--- a/res/rarelink_cdm_v2_0_0_dev0_datadictionary.csv
+++ b/res/rarelink_cdm_v2_0_0_dev0_datadictionary.csv
@@ -1,6 +1,6 @@
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,,,,,,y,,,,,"Variable:
+record_id,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,,,,,,y,,,,,"Variable:
SNOMED:422549004 | Pseudonym |
Choices: n/a
Version(s):
@@ -16,15 +16,7 @@ Version(s):
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 - for more detail please read our comprehensive User Guide
-
- - Please search for the country code using the ISO 3166 list available at: ISO 3166 Country Codes. Enter only the two or three-letter ISO country code, such as 'CAN' or 'TUR'.
- - Not all fields must be entered - If information is not known or not required, leave it blank.
-
-
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,,,,,y,,,,,"Variable:
SNOMED:184099003 | Date of Birth |
Choices: n/a
Version(s):
@@ -85,17 +77,7 @@ Version(s):
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 - for more detail please read our comprehensive User Guide
-
- - The form can be repeated to account for changes over time regarding the vital status, respective information, and undiagnosed rare disease cases.
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - For the time of death, follow the same instructions as above for when the exact month or day is unknown. (e.g., sometime in June 2022 --> 01.June.2022, sometime in 2014 --> 01.01.2014)
- - For the item ""length of gestation at birth,"" please enter only the exact weeks and days in the format: e.g., '35+6'.
- - Not all fields must be entered - If information is not known or not required, leave it blank.
-
-
RareLink - 3) Patient Status
",text,Date of Completion for the Sheet,,,date_ymd,,,,,y,,,,,
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:
@@ -160,16 +142,7 @@ Version(s):
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 - for more detail please read our comprehensive User Guide
-
- - It is also a repeated form, with one encounter per form.
- - If possible, use the dates. In relation to the Disease sheet, you can create a comprehensive overview of a patient's disease history with encounters.
- - 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)
- - Not all fields must be entered - If information is not known or not required, leave it blank.
-
-
RareLink - 4) Care Pathway
-
Notes for entering information into the Disease sheet - for more detail please read our comprehensive User Guide
-
- - It is a repeated form, you can enter as many diseases as you wish. Please only enter one disease per form, each encodable with multiple ontologies. We recommend using MONDO for disease encoding.
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - To link a disease to genetic variant(s) in Section 6.1 Genetic Findings, please also enter the same MONDO or OMIM_p codes here.
- - OMIM_g codes refer to specific genes, while OMIM_p codes refer to phenotypes or clinical manifestations associated with genetic disorders (for more information see OMIM).
- - If information for a specific field is not known, you can leave the field empty.
- - The ICD-11 is not integrated into BIOPORTAL yet. If you wish to encode diseases with ICD-11, please look them up here: ICD-11 Browser. Please only enter the codes themselves, e.g., 'AA10'.
- - The elements ""age at onset"" and ""age at diagnosis"" are derived from the ERDRI-CDS. You can select ""prenatal"" and ""birth"" at 5.3 and 5.5, while also entering the dates. If dates are available, we recommend always entering them.
- - 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).
-
-
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',y,,,,,"Variable:
SNOMED:64572001 | Disease
Choices:
@@ -370,25 +330,7 @@ Version(s):
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 - for more detail please read our comprehensive User Guide
-
- - It is a repeated form, you can enter as many variants as you wish, if desired linked with a genomic disease.
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - Not all fields must be entered - If information is not known or not required, leave it blank.
- - To link a variant to a (genetic) IEI diagnosis, please select for the corresponding IEI disease. You can also link mulitple variants with varying interpretation statuses to a disease by repeating the form.
- - OMIM_g codes refer to specific genes, while OMIM_p codes refer to phenotypes or clinical manifestations associated with genetic disorders (for more information see OMIM).
- - To capture the genetic variants, please provide validated HGVS values (HGVS Nomenclature) for genomic changes (g.HGVS), DNA sequence changes (c.HGVS), or amino acid changes (p.HGVS). We recommend entering c.HGVS before using g.HGVS or p.HGVS.
- - To validate your mutations:
-
- - You can search the mutation in ClinVar (ClinVar) or Varsome (Varsome).
- - You must enter the expression into an HGVS expression validator, such as HGVS Validator.
-
-
- - If you cannot validate your variant expressions according to HGVS expressions, please use the text field ""Unvalidated Variant Text of the mutation"" to enter all information you have for subsequent validation.
-
-
RareLink - 6.1) Genetic Findings
-
Notes for entering information into the Phenotypic Feature sheet - for more detail please read our comprehensive User Guide
-
- - It is a repeated form, you can enter as many phenotypic features as needed.
- - If the specific month or day is not known for the determination date, 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).
- - We recommend capturing the time a characteristic was observed.
- - Please always enter the status as either confirmed or refuted.
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - Encode the modifiers for more complex deep phenotyping, for instance, one or more terms from HP:0012823 (HP:0012823), the infectious agent causing the phenotype encoded with NCBITAXON, or SNOMED for other modifiers.
- - For more effective analysis with clinical modifiers, we recommend establishing consistent definitions for these modifiers within a specific cohort.
-
-
RareLink - 6.2) Phenotypic Feature
",text,6.2.1 Phenotypic Feature,BIOPORTAL:HP,An observed physical and clinical characteristic encoded with HPO.,,,,,,y,,,,,"Variable:
SNOMED:8116006 | Phenotypic Feature
Choices:
n/a
@@ -652,7 +582,7 @@ Version(s):
Mapping:
- HL7 FHIR Expression v4.0.1: Observation.Code
- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.type"
-snomed_363778006,rarelink_6_2_phenotypic_feature,,dropdown,6.2.2 Status,"snomed_410605003, Confirmed present | snomed_723511001, Refuted","The current status of the phenotypic feature, indicating whether it is confirmed or refuted.",,,,,,,,,,,"Variable:
+snomed_363778006,rarelink_6_2_phenotypic_feature,,dropdown,6.2.2 Status,"snomed_410605003, Confirmed present | snomed_723511001, Refuted","The current status of the phenotypic feature, indicating whether it is confirmed or refuted.",,,,,,y,,,,,"Variable:
SNOMED:363778006 | Status
Choices:
- SNOMED:410605003 | Confirmed present
@@ -775,45 +705,84 @@ Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.extension
- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.modifier"
phenotypicfeature_evidence,rarelink_6_2_phenotypic_feature,,text,6.2.9 Evidence for the phenotype [ECO],BIOPORTAL:ECO,The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO).,,,,,,,,,,,
-measurements_descr,rarelink_6_3_measurements,RareLink - 6.3) Measurements,descriptive,"
-
Notes and Tips for entering information into the Measurements sheet - for more detail please read our comprehensive User Guide
-
- - It is a repeated form; capture information for one measurement and repeat as many times as necessary
- - Not all fields must be entered - If information is not known or not required, leave it blank.
- - It is recommended to define a set of rules for capturing measurements within a cohort to improve subsequent analyses
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - To search in LOINC, we recommend searching here: https://loinc.org/search/ (you may have to create an account to access Loinc Search).
-
-
RareLink - 6.3) Measurements
",dropdown,6.3.0A Category,"social-history, Social History | vital-signs, Vital Signs | imaging, Imaging | laboratory, Laboratory | procedure, Procedure | survey, Survey | exam, Exam | therapy, Therapy | activity, Activity",The type of measurement performed.,,,,,,y,,,,,"Variable: measurement_category | 6.3.0 Measurement Category
+Choices:
+- social-history | Social History
+- vital-signs | Vital Signs
+- imaging | Imaging
+- laboratory | Laboratory
+- procedure | Procedure
+- survey | Survey
+- exam | Exam
+- therapy | Therapy
+- activity | Activity
+Version(s):
+- HL7 FHIR v4.0.1
+Mapping:
+- HL7 FHIR Expression v4.0.1: Obersvation.category
+- GA4GH Phenopacket Schema v2.0 Element: n/a"
+measurement_status,rarelink_6_3_measurements,,dropdown,6.3.0B Status,"registered, Registered | preliminary, Preliminary | final, Final | amended, Amended | corrected, Corrected | cancelled, Cancelled | unknown, Unknown",The status of the measurement.,,,,,[measurement_category] != 'procedure',y,,,,,"Variable: measurement_status | 6.3.0B Measurement Status
+Choices:
+- registered | Registered
+- preliminary | Preliminary
+- final | Final
+- amended | Amended
+- corrected | Corrected
+- cancelled | Cancelled
+- unknown | Unknown
+Version(s):
+- HL7 FHIR v4.0.1
+Mapping:
+- HL7 FHIR Expression v4.0.1: Obersvation.status
+- GA4GH Phenopacket Schema v2.0 Element: n/a"
+ncit_c60819,rarelink_6_3_measurements,,text,6.3.1 Assay,BIOPORTAL:LOINC,Please search the assay in LOINC and see tips above.,,,,,[measurement_category] != 'vital-signs' and [measurement_category] != 'procedure',y,,,,,"Variable: NCIT:C60819 | Assay
Choices: n/a
Version(s):
- NCIT v24.04e
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.code
- GA4GH Phenopacket Schema v2.0 Element: Measurement.assay"
-ncit_c25712,rarelink_6_3_measurements,,text,6.3.2 Value,,Please enter a two decimal number,number_2dp,0.00,999999.99,,,,,,,,"Variable: NCIT:C25712 | Value
+ln_85353_1,rarelink_6_3_measurements,,dropdown,6.3.1A Vital Signs Panel,"85353_1, Vital Signs Panel | 9279_1, Respiratory Rate [/min] | 8867_4, Heart Rate [/min] | 2708_6, Oxygen Saturation [%] | 8310_5, Body Temperature [Cel, degF] | 8302_2, Body Height [cm] | 9843_4, Head Circumference [cm] | 29463_7, Body Weight [kg] | 39156_5, Body Mass Index [kg/m2] | 8480_6, Systolic Blood Pressure [mmHg] | 8462_4, Diastolic Blood Pressure [mmHg] | other, Other",The type of vital sign measurement performed.,,,,,[measurement_category] = 'vital-signs',y,,,,,"Variable: LOINC:85353_1 | Vital Signs Panel
+Choices:
+- 9279_1, Respiratory Rate [/min]
+- 8867_4, Heart Rate [/min]
+- 2708_6, Oxygen Saturation [%]
+- 8310_5, Body Temperature [Cel, degF]
+- 8302_2, Body Height [cm]
+- 9843_4, Head Circumference [cm]
+- 29463_7, Body Weight [kg]
+- 39156_5, Body Mass Index [kg/m2]
+- 8480_6, Systolic Blood Pressure [mmHg]
+- 8462_4, Diastolic Blood Pressure [mmHg]
+- other, Other
+Version(s):
+- LOINC v2.78
+Mapping:
+- HL7 FHIR Expression v4.0.1: Observation.code
+- GA4GH Phenopacket Schema v2.0 Element: Measurement.assay"
+ln_85353_1_other,rarelink_6_3_measurements,,text,6.3.1A Other Vital Sign,BIOPORTAL:LOINC,"If not found in the list of choices above, the type of vital sign measurement performed",,,,,[ln_85353_1] = 'other',,,,,,
+ncit_c25712,rarelink_6_3_measurements,,text,6.3.2 Value,,Please enter a two decimal number,number,0.00,999999.99,,[measurement_category] != 'procedure',y,,,,,"Variable: NCIT:C25712 | Value
Choices: n/a
Version(s):
- NCIT v24.04e
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.value[x]
- GA4GH Phenopacket Schema v2.0 Element: Measurement.measurement_value"
-ncit_c92571,rarelink_6_3_measurements,,text,6.3.3 Value Unit,BIOPORTAL:UO,"Please search the unit in the Unit Ontology (UO). Tip: Search for the official abbreviations (e.g. dl, kg, l, etc.)",,,,,,,,,,,"Variable: NCIT:C92571 | Measurement Unit Description
+ncit_c92571,rarelink_6_3_measurements,,text,6.3.3 Value Unit,BIOPORTAL:UO,"Please search the unit in the Unit Ontology (UO). Tip: Search for the official abbreviations (e.g. dl, kg, l, etc.)",,,,,"([measurement_category] != 'vital-signs' or [ln_85353_1_other] <> """") and [measurement_category] != 'procedure'",y,,,,,"Variable: NCIT:C92571 | Measurement Unit Description
Choices: n/a
Version(s):
- NCIT v24.04e
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.value[x].unit
- GA4GH Phenopacket Schema v2.0 Element: Measurement.measurement_value"
-ncit_c41255,rarelink_6_3_measurements,,text,6.3.4 Interpretation,BIOPORTAL:NCIT,"Please search for an interpretation in NCIT, e.g. positive / negative, below/above reference range, etc. ",,,,,,,,,,,"Variable: NCIT:C41255 | Interpretation
+ncit_c41255,rarelink_6_3_measurements,,text,6.3.4 Interpretation,BIOPORTAL:NCIT,"Please search for an interpretation in NCIT, e.g. positive / negative, below/above reference range, etc. ",,,,,[measurement_category] != 'procedure',,,,,,"Variable: NCIT:C41255 | Interpretation
Choices: n/a
Version(s):
- NCIT v24.04e
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.interpretation
- GA4GH Phenopacket Schema v2.0 Element: Measurement.measurement_value"
-ncit_c82577,rarelink_6_3_measurements,,text,6.3.5 Time Observed,,YYYY-MM-DD,date_ymd,,,,,,,,,,"Variable: NCIT:C82577 | Test Time
+ncit_c82577,rarelink_6_3_measurements,,text,6.3.5 Time Observed,,YYYY-MM-DD,date_ymd,,,,,y,,,,,"Variable: NCIT:C82577 | Test Time
Choices:
- n/a
Version(s):
@@ -821,7 +790,15 @@ Version(s):
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Observation.effectiveDateTime
- GA4GH Phenopacket Schema v2.0 Element: Measurement.time_observed"
-snomed_122869004_ncit,rarelink_6_3_measurements,,text,6.3.6A Procedure [NCIT],BIOPORTAL:NCIT,Please search for the procedure in NCIT and see tips above.,,,,,,,,,,,"Variable: SNOMED:122869004 | Procedure
+snomed_122869004_ncit,rarelink_6_3_measurements,,text,6.3.6A Procedure [NCIT],BIOPORTAL:NCIT,Please search for the procedure in NCIT and see tips above.,,,,,[measurement_category] != 'procedure',,,,,,"Variable: SNOMED:122869004 | Procedure
+Choices:
+- n/a
+Version(s):
+- SNOMED CT v2024-09-01
+Mapping:
+- HL7 FHIR Expression v4.0.1 [Suggested]: Procedure.code
+- GA4GH Phenopacket Schema v2.0 Element: Measurement.procedure"
+snomed_122869004_snomed,rarelink_6_3_measurements,,text,6.3.6B Procedure [SNOMED],BIOPORTAL:SNOMEDCT,Please search for the procedure in SNOMED and see tips above.,,,,,[measurement_category] != 'procedure',,,,,,"Variable: SNOMED:122869004 | Procedure
Choices:
- n/a
Version(s):
@@ -829,7 +806,8 @@ Version(s):
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Procedure.code
- GA4GH Phenopacket Schema v2.0 Element: Measurement.procedure"
-snomed_122869004_snomed,rarelink_6_3_measurements,,text,6.3.6B Procedure [SNOMED],BIOPORTAL:SNOMED,Please search for the procedure in SNOMED and see tips above.,,,,,,,,,,,"Variable: SNOMED:122869004 | Procedure
+snomed_122869004_descr,rarelink_6_3_measurements,,descriptive,"If the measurement category ""procedure"" is selected, the following information will be displayed within the FHIR-IPS Procedure Profile
",BIOPORTAL:SNOMEDCT,,,,,,[measurement_category] = 'procedure',,,,,,
+snomed_122869004,rarelink_6_3_measurements,,text,6.3.7 Procedure [SNOMED],BIOPORTAL:SNOMEDCT,Please search for the procedure in SNOMED,,,,,[measurement_category] = 'procedure',y,,,,,"Variable: SNOMED:122869004 | Procedure
Choices:
- n/a
Version(s):
@@ -837,16 +815,33 @@ Version(s):
Mapping:
- HL7 FHIR Expression v4.0.1 [Suggested]: Procedure.code
- GA4GH Phenopacket Schema v2.0 Element: Measurement.procedure"
-family_history_descr,rarelink_6_4_family_history,RareLink - 6.3) Family History,descriptive,"
-
Notes for entering information into the Family History sheet - for more detail please read our comprehensive User Guide
-
- - It is a repeated form; capture information for as many family members as needed, with one family member per sheet.
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - Not all fields must be entered - If information is not known or not required, leave it blank.
- - If a pseudonym was already assigned to the specific family member, please enter it here to identify across records.
-
-
-
Notes for entering information into the Consent sheet - for more detail please read our comprehensive User Guide
-
- - Specifies consent-specific data for a patient, e.g., for registry use.
- - Provide a link to the BioBank if applicable.
-
-
-
Notes for entering information into the Disability sheet - for more detail please read our comprehensive User Guide
-
- - Enter the disability code of the ICF (International Classification of Functioning, Disability, and Health).
- - These RareLink sheets are integrated with BioPortal for ontology-specific searches. For a smoother experience when looking up terms in these fields, we recommend using the OLS platform (https://www.ebi.ac.uk/ols4/ontologies) to locate the appropriate terms for your search.
- - The data entered corresponds to the date of admission or data entry (element 1.2).
-
-