Example phenopackets

A set of example phenopackets is distributed with the phenopacket-tools binary. The example files should be used to demonstrate the tools’ functionality.

The files are grouped in sub-folders:

examples
├── convert
├── phenopackets
└── validate
  ├── base
  ├── custom-json-schema
  ├── organ-systems
  └── phenotype-validation

Convert

The convert folder contains one v1 phenopacket to demonstrate the conversion functionality:

Schreckenbach-2014-TPM3-II.2.json

The phenopacket describes a case report of a 45 years-old female diagnosed with NEMALINE MYOPATHY 1; NEM1 caused by heterozygous mutation in TPM3.

Validate

The validate directory contains files for demonstrating off-the-shelf phenopacket validation functionalities.

base - base validation functionality

The folder contains a few phenopackets for demonstrating the base validation functionality of phenopacket-tools; the validation that any phenopacket must pass.

File name	Description
missing-fields.json	An invalid phenopacket with missing id, subject.id and phenotypicFeatures[0].type.label attributes.
missing-fields-valid.json	A valid version of the above phenopacket with IDs and the label.
missing-resources.json	An invalid phenopacket with missing Resource for the NCBITaxon:9606 ontology concept used to represent organism of the subject.
missing-resources-valid.json	A valid version of the above phenopacket with the Resource for describing NCBITaxon.

custom-json-schema - validate custom requirements

A bunch of phenopackets for showing how a custom JSON schema can be used to validate user-specific requirements.

File name	Description
hpo-rare-disease-schema.json	A custom JSON schema for enforcing user-specific requirements.
marfan.no-phenotype.json	The phenopacket is invalid since it contains no phenotypic features.
marfan.no-subject.json	The phenopacket is invalid since the subject is missing.
marfan.no-time-at-last-encounter.json	The phenopacket is invalid due to missing time at last encounter.
marfan.not-hpo.json	The phenopacket is invalid because HPO terms are not used to represent phenotypic features.
marfan.json	A phenopacket that meets the custom requirements.

organ-systems - validate annotation of organ systems

Phenopackets for showing organ system validation. As an example, we work with phenopackets of patients with Marfan syndrome and we require annotation of Eye, Cardiovascular, and Respiratory organ systems either by excluding the corresponding top-level HPO term or by adding a descendent term.

The phenopackets include

File name	Description
marfan.no-abnormalities.json	A valid phenopacket of a proband with no abnormalities of the target organ systems.
marfan.all-organ-system-annotated.json	A valid phenopacket of a proband who had an abnormality of eye and cardiovascular systems but no abnormality of respiratory system. Note that it is OK to have phenotypic feature of other organ system, such as Arachnodactyly in this case.
marfan.missing-eye-annotation.json	An invalid phenopacket of a proband without any annotation of the eye.

phenotype-validation - validate custom requirements

Phenopackets for demonstrating ontology-based validation.

File name	Description
marfan.annotation-propagation-rule.json	Invalid phenopacket due to logical inconsistency in phenotypic features. The phenopacket contains both Aortic root aneurysm and its ancestor Aortic aneurysm. Only the more specific term should be used.
marfan.obsolete-term.json	The phenopacket is invalid because it contains an obsolete HPO term.
marfan.json	A phenopacket that meets the phenotype validation requirements.