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Add an example for creating a phenopacket in Python #421

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7 changes: 6 additions & 1 deletion docs/examples.rst
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Expand Up @@ -20,4 +20,9 @@ Each example has a corresponding explanation of how to create the Phenopacket us
:maxdepth: 1

Java: Rare Disease Phenopacket <rd-example-java>
Java: Cancer Phenopacket <cancer-example-java>
Java: Cancer Phenopacket <cancer-example-java>

.. toctree::
:maxdepth: 1

Python: Rare Disease Phenopacket <rd-example-python>
5 changes: 3 additions & 2 deletions docs/python.rst
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Expand Up @@ -98,8 +98,9 @@ Last, a repeated field can be set using list-like semantics:
label: "Chronic"
}

See `Protobuf documentation <https://protobuf.dev/reference/python/python-generated/#repeated-fields>`_
for more info.
`Python: Rare Disease Phenopacket <rd-example-python>`_ shows
how to build a rare phenopacket and `Protobuf documentation <https://protobuf.dev/reference/python/python-generated/#repeated-fields>`_
explains the use of the Python Protobuf bindings.


Building blocks I/O
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167 changes: 167 additions & 0 deletions docs/rd-example-python.rst
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.. _rstrarediseaseexamplepython:

#####################
Rare Disease (Python)
#####################

This page shows how to build a rare disease phenopacket
with Python bindings from the `phenopackets <https://pypi.org/project/phenopackets/>`_ package.

The phenopacket represents a case report about a boy with Bethlem myopathy
from `A complete example: Rare Disease <rd-example>`_.


***************
Building blocks
***************

We start by importing all building blocks of the Phenopacket Schema v2:

>>> from google.protobuf.timestamp_pb2 import Timestamp
>>> import phenopackets.schema.v2 as pps2

to create the building block and assemble the phenopacket.


Id
==

>>> id = "14 year-old boy"

Proband
=======

>>> subject = pps2.Individual(
... id="14 year-old boy",
... time_at_last_encounter=pps2.TimeElement(
... age=pps2.Age(
... iso8601duration="P14Y",
... )
... ),
... sex=pps2.MALE,
... )


Phenotypic features
===================

>>> evidence = pps2.Evidence(
... evidence_code=pps2.OntologyClass(
... id="ECO:0000033",
... label="author statement supported by traceable reference",
... ),
... reference=pps2.ExternalReference(
... id="PMID:30808312",
... description="COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.",
... ),
... )
>>> phenotypic_features = (
... pps2.PhenotypicFeature(
... type=pps2.OntologyClass(
... id="HP:0001558", label="Decreased fetal movement"
... ),
... onset=pps2.TimeElement(
... ontology_class=pps2.OntologyClass(
... id="HP:0011461",
... label="Fetal onset",
... ),
... ),
... evidence=(evidence,),
... ),
... pps2.PhenotypicFeature(
... type=pps2.OntologyClass(
... id="HP:0031910",
... label="Abnormal cranial nerve physiology",
... ),
... excluded=True,
... evidence=(evidence,),
... ),
... pps2.PhenotypicFeature(
... type=pps2.OntologyClass(
... id="HP:0011463",
... label="Macroscopic hematuria",
... ),
... modifiers=(
... pps2.OntologyClass(
... id="HP:0031796",
... label="Recurrent",
... ),
... ),
... onset=pps2.TimeElement(
... age=pps2.Age(
... iso8601duration="P14Y",
... ),
... ),
... evidence=(evidence,),
... ),
... pps2.PhenotypicFeature(
... type=pps2.OntologyClass(
... id="HP:0001270",
... label="Motor delay",
... ),
... severity=pps2.OntologyClass(
... id="HP:0001270",
... label="Mild",
... ),
... onset=pps2.TimeElement(
... ontology_class=pps2.OntologyClass(
... id="HP:0011463",
... label="Childhood onset",
... ),
... ),
... ),
... )


MetaData
========

>>> created = Timestamp()
>>> created.FromJsonString("2021-05-11T14:37:28.328Z")
>>> meta_data = pps2.MetaData(
... created=created,
... created_by="Peter R.",
... resources=(
... pps2.Resource(
... id="hp",
... name="human phenotype ontology",
... url="http://purl.obolibrary.org/obo/hp.owl",
... version="2018-03-08",
... namespace_prefix="HP",
... iri_prefix="http://purl.obolibrary.org/obo/HP_",
... ),
... pps2.Resource(
... id="geno",
... name="Genotype Ontology",
... url="http://purl.obolibrary.org/obo/geno.owl",
... version="19-03-2018",
... namespace_prefix="GENO",
... iri_prefix="http://purl.obolibrary.org/obo/GENO_",
... ),
... pps2.Resource(
... id="pubmed",
... name="PubMed",
... namespace_prefix="PMID",
... iri_prefix="https://www.ncbi.nlm.nih.gov/pubmed/",
... ),
... ),
... phenopacket_schema_version="2.0",
... external_references=(
... pps2.ExternalReference(
... id="PMID:30808312",
... description="Bao M, et al. COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report. BMC Neurol. 2019;19(1):32.",
... ),
... ),
... )


The phenopacket
===============

>>> proband = pps2.Phenopacket(
... id="14 year-old boy",
... subject=subject,
... phenotypic_features=phenotypic_features,
... meta_data=meta_data,
... )
>>> assert proband is not None
153 changes: 153 additions & 0 deletions python/tests/test_rd_example.py
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import typing

import pytest

import phenopackets.schema.v2 as pps2

from google.protobuf.timestamp_pb2 import Timestamp


def test_phenopacket(
subject: pps2.Individual,
phenotypic_features: typing.Sequence[pps2.PhenotypicFeature],
meta_data: pps2.MetaData,
):
"""
Test if the phenopacket from `docs/rd-example-python.rst`
can be built.
"""
proband = pps2.Phenopacket(
id="14 year-old boy",
subject=subject,
phenotypic_features=phenotypic_features,
meta_data=meta_data,
)
assert proband is not None


@pytest.fixture
def subject() -> pps2.Individual:
return pps2.Individual(
id="14 year-old boy",
time_at_last_encounter=pps2.TimeElement(
age=pps2.Age(
iso8601duration="P14Y",
)
),
sex=pps2.MALE,
)


@pytest.fixture
def evidence() -> pps2.Evidence:
return pps2.Evidence(
evidence_code=pps2.OntologyClass(
id="ECO:0000033",
label="author statement supported by traceable reference",
),
reference=pps2.ExternalReference(
id="PMID:30808312",
description="COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.",
),
)


@pytest.fixture
def phenotypic_features(
evidence: pps2.Evidence,
) -> typing.Sequence[pps2.PhenotypicFeature]:
return (
pps2.PhenotypicFeature(
type=pps2.OntologyClass(id="HP:0001558", label="Decreased fetal movement"),
onset=pps2.TimeElement(
ontology_class=pps2.OntologyClass(
id="HP:0011461",
label="Fetal onset",
),
),
evidence=(evidence,),
),
pps2.PhenotypicFeature(
type=pps2.OntologyClass(
id="HP:0031910",
label="Abnormal cranial nerve physiology",
),
excluded=True,
evidence=(evidence,),
),
pps2.PhenotypicFeature(
type=pps2.OntologyClass(
id="HP:0011463",
label="Macroscopic hematuria",
),
modifiers=(
pps2.OntologyClass(
id="HP:0031796",
label="Recurrent",
),
),
onset=pps2.TimeElement(
age=pps2.Age(
iso8601duration="P14Y",
),
),
evidence=(evidence,),
),
pps2.PhenotypicFeature(
type=pps2.OntologyClass(
id="HP:0001270",
label="Motor delay",
),
severity=pps2.OntologyClass(
id="HP:0001270",
label="Mild",
),
onset=pps2.TimeElement(
ontology_class=pps2.OntologyClass(
id="HP:0011463",
label="Childhood onset",
),
),
),
)


@pytest.fixture
def meta_data() -> pps2.MetaData:
created = Timestamp()
created.FromJsonString("2021-05-11T14:37:28.328Z")
return pps2.MetaData(
created=created,
created_by="Peter R.",
resources=(
pps2.Resource(
id="hp",
name="human phenotype ontology",
url="http://purl.obolibrary.org/obo/hp.owl",
version="2018-03-08",
namespace_prefix="HP",
iri_prefix="http://purl.obolibrary.org/obo/HP_",
),
pps2.Resource(
id="geno",
name="Genotype Ontology",
url="http://purl.obolibrary.org/obo/geno.owl",
version="19-03-2018",
namespace_prefix="GENO",
iri_prefix="http://purl.obolibrary.org/obo/GENO_",
),
pps2.Resource(
id="pubmed",
name="PubMed",
namespace_prefix="PMID",
iri_prefix="https://www.ncbi.nlm.nih.gov/pubmed/",
),
),
phenopacket_schema_version="2.0",
external_references=(
pps2.ExternalReference(
id="PMID:30808312",
description="Bao M, et al. COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report. BMC Neurol. 2019;19(1):32.",
),
),
)
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