Clinical data dictionary
175 fields in 17 sections, with types, allowed values and missing-data rules.
All fields of release 1.0. “Repeatable” sections hold a list of entries. Empty value = not recorded. Dates are ISO 8601 (YYYY-MM-DD) in exports. Numbers keep the unit recorded with them.
| Status value | Meaning (missing-data rules) |
|---|---|
| Present | Finding was assessed and is present. |
| Absent | Finding was explicitly assessed and is not present. Exported as an excluded phenotype. |
| Suspected | Finding is possible but not confirmed. Kept apart from confirmed findings; left out of ranking unless switched on. |
| Unknown | Asked or looked for, result not known. |
| Not assessed | Not examined or asked. |
| Not applicable | Cannot apply to this patient (for example by age or sex). |
| (no record) | Nothing was recorded. Never treated as absent. |
Registration and demographics
| Field | Label | Type | Allowed values |
|---|---|---|---|
| reg.hospitalId | Hospital / institution ID | text | |
| reg.studyId | Study / cohort ID | text | |
| reg.first | First name | text | |
| reg.last | Last name | text | |
| reg.dob | Date of birth | date | |
| reg.sex | Biological sex | choice | Female | Male | Intersex | Unknown |
| reg.gender | Gender identity (optional) | text | |
| reg.ancestry | Ancestry (optional) | text | |
| reg.country | Country | text | |
| reg.location | City / region | text | |
| reg.phone | Phone | text | |
| reg.email | |||
| reg.refPhys | Referring physician | text | |
| reg.geneticist | Clinical geneticist | text | |
| reg.clinician | Primary clinician | text | |
| reg.regDate | Registration date | date | |
| reg.caseType | Case type | choice | Adult | Paediatric | Neonatal | Prenatal | Deceased |
| reg.familyId | Family ID (family-based study) | text | |
| reg.dataStatus | Data collection status | choice | Not started | In progress | Complete | On hold |
| reg.dxStatus | Diagnostic status | choice | Undiagnosed | Clinical diagnosis | Molecular diagnosis | Partially explained |
| reg.indication | Referral indication | long text |
Presenting complaint (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| complaints.kind | Type | choice | Primary | Secondary |
| complaints.desc | Clinical description | long text | |
| complaints.onset | Age / date of onset | text | |
| complaints.duration | Duration | text | |
| complaints.progression | Progression | choice | Stable | Progressive | Improving | Episodic | Resolved |
| complaints.severity | Severity | choice | Borderline | Mild | Moderate | Severe | Profound |
| complaints.frequency | Frequency | choice | Constant | Frequent | Occasional | Rare | Single episode |
| complaints.associated | Associated manifestations | text | |
| complaints.triggers | Triggering / alleviating factors | text | |
| complaints.prevDx | Previous diagnoses | text | |
| complaints.source | Source of information | choice | Clinician-observed | Patient-reported | Caregiver-reported | Documented in a medical record | Derived from a test |
Medical history
| Field | Label | Type | Allowed values |
|---|---|---|---|
| med.diseases | Previous diseases | long text | |
| med.chronic | Chronic conditions | long text | |
| med.hospital | Hospitalisations | long text | |
| med.surgery | Surgeries | long text | |
| med.prevDx | Previous diagnoses | long text | |
| med.prevGenetic | Previous genetic testing | long text | |
| med.allergies | Allergies | long text | |
| med.adr | Adverse drug reactions | long text |
Medication (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| meds.name | Medication | text | |
| meds.dose | Dose and schedule | text | |
| meds.start | Start | date | |
| meds.stop | Stop | date | |
| meds.response | Treatment response | choice | Good | Partial | None | Worsened | Unknown |
| meds.adr | Adverse reaction | text |
Birth and developmental history
| Field | Label | Type | Allowed values |
|---|---|---|---|
| birth.pregnancy | Pregnancy history | long text | |
| birth.maternal | Maternal complications | long text | |
| birth.gestWeeks | Gestational age (weeks) | number | |
| birth.delivery | Delivery type | choice | Vaginal | Assisted vaginal | Elective caesarean | Emergency caesarean | Unknown |
| birth.bw | Birth weight (g) | number | |
| birth.bl | Birth length (cm) | number | |
| birth.ofc | Head circumference at birth (cm) | number | |
| birth.apgar1 | APGAR 1 min | number | |
| birth.apgar5 | APGAR 5 min | number | |
| birth.nicu | NICU admission | choice | Yes | No | Unknown |
| birth.neonatal | Neonatal complications | long text | |
| birth.congenital | Congenital abnormalities | long text | |
| birth.sat | Sat unsupported (months) | number | |
| birth.walked | Walked (months) | number | |
| birth.words | First words (months) | number | |
| birth.regression | Developmental regression | choice | Yes | No | Unknown |
| birth.intellectual | Intellectual development | long text | |
| birth.speech | Speech / language development | long text | |
| birth.motor | Motor development | long text | |
| birth.behaviour | Behavioural development | long text |
Family history (family level)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| famx.consang | Consanguinity | choice | Yes | No | Unknown |
| famx.consangDetail | Consanguinity detail | text | |
| famx.miscarriages | Miscarriages | text | |
| famx.stillbirths | Stillbirths | text | |
| famx.infantDeaths | Infant deaths | text | |
| famx.knownDisorders | Known genetic disorders in the family | long text | |
| famx.parentalAges | Parental ages at birth | text | |
| famx.ancestryNote | Relevant ancestry | text |
Relative (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| member.rel | Relationship | choice | Mother | Father | Brother | Sister | Sibling (sex unknown) | Maternal grandmother | Maternal grandfather | Paternal grandmother | Paternal grandfather | Maternal aunt | Maternal uncle | Paternal aunt | Paternal uncle | Son | Daughter | Partner | Other / uncertain |
| member.label | Name or label | text | |
| member.sex | Sex | choice | Female | Male | Unknown |
| member.vital | Vital status | choice | Alive | Deceased | Unknown |
| member.age | Age / age at death | text | |
| member.affected | Affected | choice | Yes | No | Unknown |
| member.phenotype | Phenotype | text | |
| member.onset | Age of onset | text | |
| member.tested | Testing status | choice | Not tested | Tested – positive | Tested – negative | Pending | Unknown |
| member.notes | Notes | text |
Phenotype observation (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| obs.status | Status | choice | Present | Absent | Suspected | Unknown | Not assessed | Not applicable |
| obs.source | Evidence source | choice | Clinician-observed | Patient-reported | Caregiver-reported | Documented in a medical record | Derived from a test |
| obs.onset | Age / date of onset | text | |
| obs.resolved | Resolution (age / date) | text | |
| obs.severity | Severity | choice | Borderline | Mild | Moderate | Severe | Profound |
| obs.progression | Progression | choice | Stable | Progressive | Improving | Episodic | Resolved |
| obs.frequency | Frequency | choice | Constant | Frequent | Occasional | Rare | Single episode |
| obs.laterality | Laterality | choice | Bilateral | Left | Right | Unilateral | Midline | Not applicable |
| obs.location | Anatomical location | text | |
| obs.confidence | Confidence | choice | High | Moderate | Low |
| obs.notes | Clinical notes / source text | long text |
Clinical examination (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| exam.type | Examination | choice | General physical | Neurological | Cardiovascular | Respiratory | Abdominal | Musculoskeletal | Dysmorphology | Ophthalmological | Dermatological | Growth assessment |
| exam.date | Date | date | |
| exam.examiner | Examiner | text | |
| exam.source | Evidence source | choice | Clinician-observed | Patient-reported | Caregiver-reported | Documented in a medical record | Derived from a test |
| exam.findings | Findings | long text | |
| exam.interp | Clinical interpretation | long text |
Examination measurement (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| meas.name | Measurement | text | |
| meas.value | Value | number | |
| meas.unit | Unit | text | |
| meas.lo | Reference low | number | |
| meas.hi | Reference high | number |
Laboratory result (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| lab.panel | Category | choice | Complete blood count | Biochemical profile | Liver function | Renal function | Electrolytes | Thyroid function | Hormonal | Immunological assay | Metabolic | Amino acid profile | Organic acid profile | Enzyme assay | Cytogenetics | Chromosomal microarray | Karyotype | Molecular diagnostic test |
| lab.test | Test name | text | |
| lab.code | Code (e.g. LOINC) | text | |
| lab.value | Value | text | |
| lab.unit | Unit | text | |
| lab.lo | Reference low | number | |
| lab.hi | Reference high | number | |
| lab.flag | Abnormal flag | choice | Auto | Normal | Low | High | Abnormal |
| lab.sample | Sample type | text | |
| lab.collected | Collected | datetime-local | |
| lab.lab | Laboratory | text | |
| lab.method | Method | text | |
| lab.interp | Interpretation | long text |
Genomic test (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| test.type | Test | choice | Gene panel | Whole-exome sequencing | Whole-genome sequencing | RNA sequencing | Mitochondrial genome | CNV analysis | Structural variant analysis | Repeat expansion analysis | Methylation profiling |
| test.lab | Laboratory | text | |
| test.date | Date | date | |
| test.status | Status | choice | Planned | Sample received | In analysis | Reported – positive | Reported – negative | Reported – inconclusive |
| test.assembly | Genome assembly | choice | GRCh38 | GRCh37 | T2T-CHM13 |
| test.panel | Panel code (if panel) | text | |
| test.result | Result summary | long text |
Data file reference (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| file.kind | File type | choice | FASTQ | BAM | CRAM | VCF | gVCF | Annotated VCF | CNV / SV file | Interpretation report | Clinical image | Other document |
| file.uri | Location (URI / path in secure storage) | text | |
| file.sha256 | SHA-256 checksum | text | |
| file.size | Size | text | |
| file.consent | Consent covers this file | choice | Yes | No | Unknown |
| file.note | Note | text |
Genomic variant (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| variant.gene | Gene symbol | text | |
| variant.geneId | Gene ID (HGNC / Ensembl) | text | |
| variant.assembly | Assembly | choice | GRCh38 | GRCh37 |
| variant.chrom | Chromosome | text | |
| variant.pos | Position | number | |
| variant.ref | Ref allele | text | |
| variant.alt | Alt allele | text | |
| variant.hgvsc | HGVS c. | text | |
| variant.hgvsp | HGVS p. | text | |
| variant.zyg | Zygosity | choice | Heterozygous | Homozygous | Hemizygous | Compound heterozygous | Mosaic | Heteroplasmic |
| variant.ab | Allele balance | number | |
| variant.consequence | Consequence | text | |
| variant.inheritance | Inheritance model | choice | Autosomal dominant | Autosomal recessive | X-linked | Mitochondrial | De novo | Unknown |
| variant.af | Population frequency | text | |
| variant.afSource | Frequency source | text | |
| variant.clinvar | ClinVar classification | text | |
| variant.clinvarReview | ClinVar review status | text | |
| variant.acmg | ACMG/AMP class | choice | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign |
| variant.criteria | ACMG criteria applied | text | |
| variant.analyst | Analyst | text | |
| variant.date | Interpretation date | date | |
| variant.evFor | Supporting evidence | long text | |
| variant.evAgainst | Conflicting evidence | long text |
Clinical document (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| doc.title | Title | text | |
| doc.type | Document type | choice | Clinical note | Discharge summary | Physician report | Referral letter | Patient-reported description | Caregiver-reported description | Laboratory / diagnostic report |
| doc.date | Date | date | |
| doc.author | Author | text | |
| doc.text | Text | long text |
Follow-up visit (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| follow.date | Date | date | |
| follow.clinician | Clinician | text | |
| follow.status | Status | choice | Scheduled | Completed | Missed | Lost to follow-up |
| follow.summary | Summary | long text | |
| follow.newFindings | New or changed findings | long text | |
| follow.plan | Plan | long text | |
| follow.next | Next follow-up | date |
Consent record (repeatable)
| Field | Label | Type | Allowed values |
|---|---|---|---|
| consent.type | Consent for | choice | Clinical genetic testing | Research use | Data sharing (de-identified) | Clinical images | Recontact | Secondary findings |
| consent.status | Status | choice | Given | Declined | Withdrawn | Pending |
| consent.date | Date | date | |
| consent.version | Form version | text | |
| consent.by | Given by | choice | Patient | Parent / guardian | Legal representative |
| consent.witness | Witness / recorded by | text | |
| consent.withdrawn | Withdrawal date | date | |
| consent.notes | Notes | text |
HPO annotation (attached to an observation)
| Field | Meaning |
|---|---|
| hpo | HPO identifier, e.g. HP:0001250 |
| label | Preferred label at the time of annotation |
| status | Candidate | Accepted | Rejected | Superseded |
| conf | Confidence (0–1 for extracted suggestions) |
| annotator | Person who made or accepted the annotation |
| date | Annotation date |
| ver | HPO release used |
| origin | manual | template | suggested | ai-reviewed | migration | import |
| replaces | Older identifier this annotation supersedes (migration only) |
HPO export columns (TSV / CSV)
| Column | Source |
|---|---|
| PATIENT_ID | Patient ID, or research key in de-identified exports |
| OBSERVATION_ID | Internal observation identifier |
| HPO_ID / HPO_TERM | Annotation; empty ID with the original text when unmapped |
| OBSERVATION_STATUS | Present, Absent, Suspected, Unknown, Not assessed, Not applicable |
| AGE_OF_ONSET, SEVERITY, FREQUENCY, LATERALITY | Observation fields |
| EVIDENCE_SOURCE | Who or what the finding comes from |
| CLINICAL_NOTES, ANNOTATOR | Left empty in de-identified exports |
| ANNOTATION_DATE, HPO_VERSION | Provenance |
| REVIEW_STATUS | Accepted, Candidate, Superseded or Unmapped |
© Tribro-Omics · Clinical data dictionary · Version 1.0 · 11 November 2026