Conceptual Model

Overview

To support the interoperability of family health history data within and between existing standards (such as HL7 FHIR and Phenopackets), the GA4GH Clinical and Phenotypic Data Capture Workstream developed the Pedigree Conceptual Model.

The Pedigree Conceptual Model defines core concepts and their properties, and is based on A Recommendation for The Common Data Set for Family Health History.

Concepts

The diagram below shows an overview of the pedigree concepts. Lines between concepts indicate composition.

Individual

The Individual concept represents an individual person or patient who is a member of the pedigree being investigated.

Field	Multiplicity	Description
id	1..1	External identifier for the individual
sex	1..1	Sex assigned at birth
karyotypicSex	0..1	The chromosomal sex of the individual; See Phenopacket KaryotypicSex.
gender	0..1	Presumed or reported gender identity
name	0..1	Name of the individual
dateOfBirth	0..1	Birth date of the individual, can be just birth year in most cases
age	0..1	Age of the individual, can be either Age, Estimated Age (or Ontology Class), Age Range, and/or Gestational Age; See also Phenopackets’ TimeElement.
populationDescriptors	0..*	Information about the individual’s ancestry, ethnicity, race, tribe, etc.,; terms from the Human Ancestry Ontology (HANCESTRO) are recommended, but freetext must be supported
deceased	0..1	The presumed/accepted life status of the individual as of the pedigree collection date
affected	0..1	Whether or not the individual is affected

Relationship

The Relationship concept represents the relationship that one individual has to another individual.

Field	Multiplicity	Description
individual	1..1	Identifier of the subject `Individual`; equivalent to the Biolink “subject”
relation	1..1	The relationship the `individual` has to the `relative` (e.g., if the `individual` is the `relative`’s biological mother, then relation could be `isBiologicalMotherOf` `[KIN:027]`); terms should come from the KIN Ontology.
relative	1..1	Identifier of the relative `Individual`; equivalent to the Biolink “object”

Pedigree

A Pedigree is a set of individuals and the relationships between them.

Field	Multiplicity	Description
id	1..1	External identifier for the family being investigated
indexPatients	0..*	Identified `Individual` in the family of a health condition of focus being investigated: `Proband`, `Consultand`, `First Person Tested Positive`
individuals	0..*	Collection of `Individual` who are the members of this pedigree
relationships	0..*	Collection of `Relationship` between the `individuals` who are the members of this pedigree
status	0..1	Status of the pedigree resource collection
narrative	0..1	Summary of the pedigree resource for human interpretation
date	0..1	The date the pedigree was collected or last updated, as ISO full or partial date, i.e. `YYYY`, `YYYY-MM`, or `YYYY-MM-DD`

Design motivations

Design motivation:

avoid overlap with other standards (fhir, phenopacket)
focus on relationship
graphical model, bringing relationships as top-level entities
allow for the synthesizing of patient-reported family history data, such as comes out of family history questionnaires and EHR records (and can be represented with the FamilyMemberHistoryResource), and support this information through to risk models
provide a standard interface for validation
facilitate conversion among existing standards for pedigree data

Relationships between individuals are standardized using concepts from the newly developed Kinship Ontology. To allow existing workflows and tools to gracefully add interoperability with this standard, we developed an open-source pedigree data interoperability library, pedigree-tools.