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.

Overview of concepts

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.