Pedigree

docs/ga4gh-interoperability.rst

@@ -0,0 +1,8 @@
+######################
+GA4GH Interoperability
+######################
+
+.. toctree::
+   :maxdepth: 1
+
+   GA4GH Pedigree Standard <ga4gh-pedigree>

docs/ga4gh-pedigree.rst

@@ -0,0 +1,108 @@
+.. _rsga4ghpedigree:
+
+##############
+GA4GH Pedigree
+##############
+
+
+The Phenopacket-schema includes an implementation of the `GA4GH Pedigree Standard <https://pedigree.readthedocs.io/en/latest/index.html>`_.
+GA4GH Pedigree defines a conceptual model of individuals and their relationships to allow other standards, such as
+Phenopackets to be able to create an implementation of this model using native concepts. For example, the Phenopacket
+schema representation of an individual in the GA4GH Pedigree is a :ref:`rstphenopacket`.
+
+The GA4GH Pedigree Standard enables much greater expressivity of the relationships between individuals compared to the
+PED model used in the :ref:`rstfamily` message due to defining the relationships using the `Kinship ontology (KIN) <http://purl.org/ga4gh/kin.owl>`_
+
+
+Data model
+##########
+
+The data model described here is transcribed from the `documentation <https://pedigree.readthedocs.io/en/latest/pedigree-model.html#pedigree>`_
+
+Pedigree
+========
+
+.. csv-table::
+   :header: Field, Type, Multiplicity, Description
+
+   id, string, 1..1, External identifier for the family being investigated
+   narrative, string, 0..1, Summary of the pedigree resource for human interpretation
+   date, string, 0..1, The date the pedigree was collected or last updated as ISO full or partial date i.e. YYYY or YYYY-MM or YYYY-MM-DD
+   status, string, 0..1, Status of the pedigree resource collection
+   index_patients, string, 0..*, Identified Individual(s) in the family of a health condition of focus being investigated.
+   individuals, :ref:`rstphenopacket`, 0..*, Collection of Individual who are the members of this pedigree
+   relationships, :ref:`rstga4ghrelationship`, 0..*, Collection of Relationship between the individuals who are the members of this pedigree
+
+
+index_patients
+~~~~~~~~~~~~~~
+
+A list of identifiers for the individual(s) in the family affected with the health condition being investigated. These
+individuals(s) are often termed the Proband, Consultand or First Person Tested Positive.
+
+
+.. _rstga4ghrelationship:
+
+Relationship
+============
+
+.. csv-table::
+   :header: Field, Type, Multiplicity, Description
+
+   individual, string, 1..1, Identifier of the subject Individual; equivalent to the Biolink "subject"
+   relation, :ref:`rstontologyclass`, 1..1, The relationship the individual has to the relative.
+   relative, string, 1..1, Identifier of the relative Individual; equivalent to the Biolink "object"
+
+
+individual and relative
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The identifier values used in the ``individual`` and ``relative`` fields **must** match a value in the **id** element
+used in the :ref:`rstindividual` ``subject`` of the phenopackets listed in the ``pedigree`` ``individuals`` field.
+
+relation
+~~~~~~~~
+
+An :ref:`rstontologyclass` from the `KIN Ontology <http://purl.org/ga4gh/kin.owl>`_ indicating the relationship the
+``individual`` has to the ``relative`` e.g. if the individual is the relative's biological mother, then relation should
+be isBiologicalMotherOf [KIN:027].
+
+
+Example
+#######
+
+In this example we have simplified the phenopackets to include only the minimum required information to make a pedigree.
+Ordinarily there should be more fields (e.g. the :ref:`rstmetadata`) within the phenopacket.
+
+.. code-block:: yaml
+
+    ---
+    id: "FAM1"
+    narrative: "A Phenopacket GA4GH Pedigree of a trio with an affected child"
+    date: "2022-06-23"
+    indexPatients:
+    - "CHILD"
+    individuals:
+    - id: "1"
+      subject:
+        id: "MOTHER"
+        sex: "FEMALE"
+    - id: "2"
+      subject:
+        id: "FATHER"
+        sex: "MALE"
+    - id: "3"
+      subject:
+        id: "CHILD"
+    relationships:
+    - individualId: "MOTHER"
+      relation:
+        id: "KIN:027"
+        label: "isBiologicalMother"
+      relativeId: "CHILD"
+    - individualId: "FATHER"
+      relation:
+        id: "KIN:028"
+        label: "isBiologicalFather"
+      relativeId: "CHILD"
+

docs/index.rst

@@ -29,4 +29,4 @@ use `this link <https://phenopacket-schema.readthedocs.io/en/1.0.0/>`_.
    recommended-ontologies
    working
    examples
-
+   ga4gh-interoperability

pom.xml

@@ -212,8 +212,9 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.22.2</version>
+                <version>3.0.0-M7</version>
                 <configuration>
+                    <useModulePath>false</useModulePath>
                     <excludes>
                         <exclude>**/FooTest.java</exclude>
                     </excludes>

src/main/java/module-info.java

@@ -9,4 +9,6 @@
 
     exports org.ga4gh.vrs.v1;
     exports org.ga4gh.vrsatile.v1;
+
+    exports org.ga4gh.pedigree.v1;
 }

src/main/proto/ga4gh/pedigree/v1/pedigree.proto

@@ -0,0 +1,49 @@
+syntax = "proto3";
+
+package org.ga4gh.pedigree.v1;
+
+import "phenopackets/schema/v2/phenopackets.proto";
+import "phenopackets/schema/v2/core/base.proto";
+
+option java_multiple_files = true;
+option java_package = "org.ga4gh.pedigree.v1";
+
+// A GA4GH Pedigree - equivalent to the Phenopacket::Family message
+message Pedigree {
+
+  // External identifier for the family being investigated
+  string id = 1;
+
+  // Summary of the pedigree resource for human interpretation
+  string narrative = 2;
+
+  // The date the pedigree was collected or last updated, as ISO full or partial date, i.e. YYYY, YYYY-MM, or YYYY-MM-DD
+  string date = 3;
+
+  // Status of the pedigree resource collection
+  string status = 5;
+
+  // Identified Individual in the family of a health condition of focus being investigated: Proband, Consultand,
+  // First Person Tested Positive
+  repeated string index_patients = 6;
+
+  // Collection of Individual who are the members of this pedigree
+  repeated org.phenopackets.schema.v2.Phenopacket individuals = 7;
+
+  // Collection of Relationship between the individuals who are the members of this pedigree
+  repeated Relationship relationships = 8;
+
+}
+
+message Relationship {
+  // Identifier of the subject Individual; equivalent to the Biolink "subject"
+  string individual_id = 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 (http://purl.org/ga4gh/kin.owl).
+  org.phenopackets.schema.v2.core.OntologyClass relation = 2;
+
+  // Identifier of the relative Individual; equivalent to the Biolink "object"
+  string relative_id = 3;
+}