Open Pedigree is a robust browser-based genomic pedigree drawing solution using Prototype, Raphaël, and PhenoTips.

✔ Robust support for complext families, intergenerational linkages, and consanguinity

✔ Shade nodes with disorders and/or candidate genes

✔ Quickly start with family templates

✔ Automatic consanguinity detection

✔ Import from PED, LINKAGE, GEDCOM (Cyrillic), or BOADICEA

Quickly get started with open pedigree on your computer:

git clone [email protected]:phenotips/open-pedigree.git
cd open-pedigree
npm install
npm start

Open a browser to https://localhost:9000/

Contributions welcome! Fork the repository and create a pull request to share your improvements with the community.

In order to ensure that the licensing is clear and stays open, you'll be asked to sign a CLA with your first pull request.

This is free software! Create an issue in GitHub to ask others for help, or try fixing the issue yourself and then make a pull request to contribute it back to the core.

For commercial support or for information about the paid Enterprise version, please contact Gene42.

Copyright (c) 2019 Gene42 Inc.

Open Pedigree is distributed under the LGPL-2.1 (GNU Lesser General Public License).

You can easily comply with this license by:

• including prominent notice of the use of Open Pedigree in your software that uses it
• retaining all copyright notices in the software
• ensuring that any and all changes you make to the software are disclosed and open-sourced under the LGPL

The FHIR import/export does not have an actual specification to follow. There is a specification in development, though we have deviated from it, choosing to use a Composition so that the family history resources and observations can be bundled together, rather then the List of family history resources in the current specification. Not all data gathered by the editor has a mapping in the FHIR representation. This means that any data with no mapping will be lost. Some other aspects of the mapping also do not translate directly, where possible naming conventions are used to try and account for these. For example the FHIR FamilyHistory resource has a single name field which is a string. The pedigree editor has a first name, last name and a last name at birth, this will be written into the FamilyHistory resource as (). When importing the FHIR resource everything but the last word is the first name and a trailing name in brackets will be taken as last name at birth.

• Heredity options - This can be 'Childless' or 'Infertile' in the editor, this is added as an Observation resource with a predefined name. If the name doesn't match, then the field won't be populated.

• Carrier Status - This can be 'Carrier' or 'Pre-symptomatic' in the editor, this is added as an Observation resource with a predefined name. If the name doesn't match, then the field won't be populated.

• Evaluated - This is a checkbox in the editor, but is not currently stored on the fhir resource.

• Lost Contact - This is a checkbox in the editor, but is not currently stored on the fhir resource.

• Multiple Sibling Nodes - In the editor you can create a single node to represent multiple siblings, at the moment these will be saved as a single familiy history resource with no name and the number of siblings will be lost.

• Phenotype and Candidate Genes are both stored as Observation Resources associated with a family history resource. The system uses a naming convention to distinguish the two, otherwise it tries to match the code system to try and determine if the observation represents a Phenotype or Candidate gene.

• Life status - This can be 'unborn', 'stillborn' and 'aborted' with an associated gestation age. This will be written into the deceasedString field on the family history resource in a form like 'stillborn 34 weeks'.

The fhir format now includes a DocumentReference resource which contains an attachement of an svg representation of the pedigree diagram.