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Merge pull request #3 from ielis/release-0.2.1
Release `0.2.1`
2 parents d381b56 + 09749f7 commit 0c92952

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‎Cargo.toml‎

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[package]
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name = "phenopackets-dev"
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version = "0.2.0"
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authors = [
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"Daniel Danis", "Daniel Danis <daniel.gordon.danis@protonmail.com>",
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]
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version = "0.2.1"
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authors = ["Daniel Danis", "Daniel Danis <daniel.gordon.danis@protonmail.com>"]
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edition = "2021"
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description = "Rust bindings for Phenopacket Schema"
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readme = "README.md"
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prost-types = "0.13"
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[build-dependencies]
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prost-build = "0.13"
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prost-build = "0.13"

‎README.md‎

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# Phenopacket Schema
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[![Continuous Integration](https://github.com/ielis/phenopackets-dev/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/ielis/phenopackets-dev/actions/workflows/ci.yml?query=branch%3Amaster)
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[![Documentation](https://docs.rs/phenopackets-dev/badge.svg)](https://docs.rs/phenopackets-dev/)
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[![Crate](https://img.shields.io/crates/v/phenopackets-dev.svg)](https://crates.io/crates/phenopackets-dev)
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Rust bindings for Phenopacket Schema.
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# Rust bindings for Phenopacket Schema
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See the documentation on [docs.rs](https://docs.rs/phenopackets-dev/latest/phenopackets_dev/)
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for usage examples and more info.

‎data/v1/README.md‎

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# README
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The files in this folder correspond to comprehensive, albeit medically invalid, phenopacket elements:
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- phenopacket
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- family, or
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- cohort.
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The content corresponds to the output of `TestData.V1.comprehensive*()` as of Oct 27th, 2022
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(see [TestData](https://github.com/phenopackets/phenopacket-tools/blob/main/phenopacket-tools-test/src/main/java/org/phenopackets/phenopackettools/test/TestData.java) in phenopacket-tools).

‎data/v1/cohort.json‎

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{
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"id": "comprehensive-cohort-id",
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"description": "A description of the example cohort.",
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"members": [{
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"id": "comprehensive-phenopacket-id",
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"subject": {
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"id": "14 year-old boy",
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"alternateIds": ["boy", "patient", "proband"],
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"dateOfBirth": "1970-01-02T10:17:36.000000100Z",
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"ageAtCollection": {
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"age": "P14Y"
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},
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"sex": "MALE",
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"karyotypicSex": "XY",
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"taxonomy": {
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"id": "NCBITaxon:9606",
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"label": "homo sapiens"
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}
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},
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"phenotypicFeatures": [{
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"type": {
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"id": "HP:0001558",
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"label": "Decreased fetal movement"
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},
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"classOfOnset": {
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"id": "HP:0011461",
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"label": "Fetal onset"
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},
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"evidence": [{
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"evidenceCode": {
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"id": "ECO:0000033",
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"label": "author statement supported by traceable reference"
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},
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"reference": {
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"id": "PMID:30808312",
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"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
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}
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}]
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}, {
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"type": {
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"id": "HP:0031910",
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"label": "Abnormal cranial nerve physiology"
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},
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"negated": true,
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"evidence": [{
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"evidenceCode": {
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"id": "ECO:0000033",
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"label": "author statement supported by traceable reference"
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},
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"reference": {
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"id": "PMID:30808312",
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"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
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}
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}]
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}, {
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"type": {
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"id": "HP:0011463",
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"label": "Macroscopic hematuria"
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},
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"modifiers": [{
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"id": "HP:0031796",
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"label": "Recurrent"
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}],
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"ageOfOnset": {
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"age": "P14Y"
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},
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"evidence": [{
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"evidenceCode": {
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"id": "ECO:0000033",
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"label": "author statement supported by traceable reference"
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},
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"reference": {
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"id": "PMID:30808312",
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"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
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}
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}]
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}, {
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"type": {
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"id": "HP:0001270",
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"label": "Motor delay"
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},
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"severity": {
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"id": "HP:0012825",
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"label": "Mild"
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},
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"classOfOnset": {
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"id": "HP:0011463",
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"label": "Childhood onset"
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}
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}],
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"biosamples": [{
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"id": "biosample-id",
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"individualId": "14 year-old boy",
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"description": "Muscle biopsy of 14 year-old boy",
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"sampledTissue": {
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"id": "UBERON:0003403",
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"label": "skin of forearm"
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},
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"taxonomy": {
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"id": "NCBITaxon:9606",
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"label": "homo sapiens"
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},
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"ageOfIndividualAtCollection": {
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"age": "P14Y"
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},
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"histologicalDiagnosis": {
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"id": "NCIT:C38757",
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"label": "Negative Finding"
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},
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"tumorProgression": {
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"id": "NCIT:C3677",
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"label": "Benign Neoplasm"
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},
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"tumorGrade": {
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"id": "NCIT:C28076",
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"label": "Disease Grade Qualifier"
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},
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"diagnosticMarkers": [{
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"id": "NCIT:C68748",
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"label": "HER2/Neu Positive"
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}]
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}],
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"genes": [{
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"id": "HGNC1:3688",
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"symbol": "FGFR1"
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}],
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"variants": [{
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"hgvsAllele": {
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"hgvs": "NM_001848.2:c.877G\u003eA"
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},
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"zygosity": {
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"id": "GENO:0000135",
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"label": "heterozygous"
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}
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}],
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"diseases": [{
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"term": {
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"id": "OMIM:101600",
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"label": "PFEIFFER SYNDROME"
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},
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"classOfOnset": {
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"id": "HP:0003577",
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"label": "Congenital onset"
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}
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}],
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"htsFiles": [{
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"uri": "file://data/genomes/P000001C",
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"description": "Whole genome sequencing VCF output",
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"htsFormat": "VCF",
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"genomeAssembly": "GRCh38.p13",
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"individualToSampleIdentifiers": {
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"14 year-old boy": "P000001C"
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}
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}],
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"metaData": {
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"created": "2022-10-03T16:39:04.000123456Z",
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"createdBy": "Peter R.",
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"submittedBy": "PhenopacketLab",
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"resources": [{
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"id": "hp",
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"name": "human phenotype ontology",
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"url": "http://purl.obolibrary.org/obo/hp.owl",
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"version": "2018-03-08",
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"namespacePrefix": "HP",
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"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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}, {
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"id": "geno",
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"name": "Genotype Ontology",
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"url": "http://purl.obolibrary.org/obo/geno.owl",
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"version": "19-03-2018",
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"namespacePrefix": "GENO",
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"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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}, {
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"id": "pubmed",
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"name": "PubMed",
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"namespacePrefix": "PMID",
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"iriPrefix": "https://www.ncbi.nlm.nih.gov/pubmed/"
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}, {
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"id": "ncit",
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"name": "NCI Thesaurus",
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"url": "http://purl.obolibrary.org/obo/ncit.owl",
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"version": "20-03-2020",
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"namespacePrefix": "NCIT",
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"iriPrefix": "http://purl.obolibrary.org/obo/NCIT_"
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}],
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"phenopacketSchemaVersion": "1.0.0",
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"externalReferences": [{
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"id": "PMID:30808312",
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"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
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}]
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}
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}, {
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"subject": {
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"id": "MOTHER",
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"sex": "FEMALE"
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}
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}, {
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"subject": {
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"id": "FATHER",
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"sex": "MALE"
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}
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}],
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"htsFiles": [{
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"uri": "file://data/genomes/FAM000001",
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"description": "Whole genome sequencing VCF output",
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"htsFormat": "VCF",
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"genomeAssembly": "GRCh38.p13",
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"individualToSampleIdentifiers": {
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"14 year-old boy": "P000001C",
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"MOTHER": "P000001M",
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"FATHER": "P000001F"
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}
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}],
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"metaData": {
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"created": "2022-10-03T16:39:04.000123456Z",
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"createdBy": "Peter R.",
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"submittedBy": "PhenopacketLab",
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"resources": [{
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"id": "hp",
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"name": "human phenotype ontology",
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"url": "http://purl.obolibrary.org/obo/hp.owl",
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"version": "2018-03-08",
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"namespacePrefix": "HP",
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"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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}, {
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"id": "geno",
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"name": "Genotype Ontology",
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"url": "http://purl.obolibrary.org/obo/geno.owl",
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"version": "19-03-2018",
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"namespacePrefix": "GENO",
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"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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}, {
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"id": "pubmed",
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"name": "PubMed",
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"namespacePrefix": "PMID",
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"iriPrefix": "https://www.ncbi.nlm.nih.gov/pubmed/"
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}, {
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"id": "ncit",
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"name": "NCI Thesaurus",
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"url": "http://purl.obolibrary.org/obo/ncit.owl",
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"version": "20-03-2020",
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"namespacePrefix": "NCIT",
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"iriPrefix": "http://purl.obolibrary.org/obo/NCIT_"
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}],
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"phenopacketSchemaVersion": "1.0.0",
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"externalReferences": [{
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"id": "PMID:30808312",
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"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
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}]
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}
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}

‎data/v1/cohort.pb‎

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comprehensive-cohort-id$A description of the example cohort.�
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comprehensive-phenopacket-id\
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14 year-old boyboypatientproband��d"
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P14Y08B
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NCBITaxon:9606 homo sapiens�&
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HP:0001558Decreased fetal movementJ
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HP:0011461 Fetal onsetR�
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@
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ECO:00000331author statement supported by traceable referencee
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PMID:30808312TCOL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.�/
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HP:0031910!Abnormal cranial nerve physiologyR�
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@
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ECO:00000331author statement supported by traceable referencee
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PMID:30808312TCOL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.�#
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HP:0011463Macroscopic hematuria*
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HP:0031796 Recurrent2
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P14YR�
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@
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ECO:00000331author statement supported by traceable referencee
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PMID:30808312TCOL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.N
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HP:0001270 Motor delay"
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HP:0012825MildJ
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HP:0011463Childhood onset"�
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biosample-id14 year-old boy Muscle biopsy of 14 year-old boy"!
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UBERON:0003403skin of forearm2
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NCBITaxon:9606 homo sapiens:
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P14YJ
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NCIT:C38757Negative FindingR
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NCIT:C3677Benign NeoplasmZ&
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NCIT:C28076Disease Grade Qualifierb
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NCIT:C68748HER2/Neu Positive*
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HGNC1:3688FGFR126NM_001848.2:c.877G>A2
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GENO:0000135 heterozygous:B
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OMIM:101600PFEIFFER SYNDROME"
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HP:0003577Congenital onsetBm
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file://data/genomes/P000001C"Whole genome sequencing VCF output"
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GRCh38.p13*
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14 year-old boyP000001CJ�
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�����Peter R.PhenopacketLab"y
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hphuman phenotype ontology%http://purl.obolibrary.org/obo/hp.owl"
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2018-03-08*HP2"http://purl.obolibrary.org/obo/HP_"z
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genoGenotype Ontology'http://purl.obolibrary.org/obo/geno.owl"
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19-03-2018*GENO2$http://purl.obolibrary.org/obo/GENO_"<
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pubmedPubMed*PMID2$https://www.ncbi.nlm.nih.gov/pubmed/"v
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ncitNCI Thesaurus'http://purl.obolibrary.org/obo/ncit.owl"
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20-03-2020*NCIT2$http://purl.obolibrary.org/obo/NCIT_21.0.0:e
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PMID:30808312TCOL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report. 
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MOTHER0 
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FATHER0"�
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file://data/genomes/FAM000001"Whole genome sequencing VCF output"
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GRCh38.p13*
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14 year-old boyP000001C*
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MOTHERP000001M*
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FATHERP000001F*�
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�����Peter R.PhenopacketLab"y
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hphuman phenotype ontology%http://purl.obolibrary.org/obo/hp.owl"
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2018-03-08*HP2"http://purl.obolibrary.org/obo/HP_"z
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genoGenotype Ontology'http://purl.obolibrary.org/obo/geno.owl"
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19-03-2018*GENO2$http://purl.obolibrary.org/obo/GENO_"<
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pubmedPubMed*PMID2$https://www.ncbi.nlm.nih.gov/pubmed/"v
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ncitNCI Thesaurus'http://purl.obolibrary.org/obo/ncit.owl"
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20-03-2020*NCIT2$http://purl.obolibrary.org/obo/NCIT_21.0.0:e
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PMID:30808312TCOL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report.

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