| Next changeset 1:89cbbb7821b0 (2024-04-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a |
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added:
csv2xlsx.xml macros.xml test-data/Beacon-v2-Models_template.xlsx test-data/EGAF00005572721.json test-data/EGAF00005572724.json test-data/EGAF00005572727.json test-data/EGAF00005572747.json test-data/EGAF00005572750.json test-data/EGAF00005572753.json test-data/EGAF00005572756.json test-data/EGAF00005572759.json test-data/EGAF00005572762.json test-data/EGAF00005572861.json test-data/EGAF00005572881.json test-data/EGAF00005572884.json test-data/EGAF00005572887.json test-data/EGAF00005572890.json test-data/EGAF00005572893.json test-data/EGAF00005572896.json test-data/EGAF00005572899.json test-data/EGAF00005572902.json test-data/analyses.csv test-data/bff_validation.text test-data/biosamples.csv test-data/cohorts.csv test-data/datasets.csv test-data/genomicVariations.csv test-data/genomicVariationsVcf.json test-data/individuals.csv test-data/individuals.json test-data/merge_output_1.vcf.gz test-data/runs.csv test-data/runs.json test-data/test.vcf.gz |
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| diff -r 000000000000 -r ba4ed464f8b6 csv2xlsx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/csv2xlsx.xml Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,47 @@ +<tool id="beacon2_csv2xlsx" name="Beacon2 CSV2XLSX" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>v2 CSV Models to XLSX</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <expand macro="creators"/> + <command detect_errors="exit_code"><![CDATA[ + #import re + #set $names = [] + #set $x=1 + #for $x, $csv in enumerate($csvs): + #set $name_base = re.sub('[^\w\-_\.]', '_', $csv.element_identifier) + #set $name = $name_base + #silent $names.append( $name ) + ln -s '$csv' ${name} && + #end for + csv2xlsx + #for $name in $names: + ${name} + #end for + -o Beacon-v2-Models_template.xlsx + ]]></command> + <inputs> + <param name="csvs" type="data" multiple="true" format="csv" label="CSV files" help="" /> + </inputs> + <outputs> + <data name="Beacon_v2_Models_template" format="xlsx" label="${tool.name} on ${on_string}: Beacon-v2-Models_template file" from_work_dir="Beacon-v2-Models_template.xlsx" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="csvs" ftype="csv" value="analyses.csv,genomicVariations.csv,runs.csv,datasets.csv,biosamples.csv,individuals.csv,cohorts.csv" /> + <output name="Beacon_v2_Models_template" file="Beacon-v2-Models_template.xlsx" compare="sim_size"> + <assert_contents><has_size value="12000" delta="1000" /></assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + The Tool converts the data from multiple CSV files to the hierarchical structure of the Beacon v2 Models and creates an Excel file with seven entities. + The Models entities are (analyses, biosamples, cohorts, datasets, genomicVariations, individuals and runs). The Excel consisting of all Models properties ‘flattened-out’ + The Excel file is separated into seven sheets (one per entry type). The user is responsible for filling out the Excel according to the entities and terms they want to share. + Once the sheets are filled out, the Beacon v2 Reference Implementation comes with a utility that validates the Excel file against the Models JSON Schemas, and, if successful, it creates a set of JSON text + files (JSON arrays) as an output that will be later loaded into the database. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r ba4ed464f8b6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.0.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">beacon2-ri-tools</requirement> + <requirement type="package" version="1.12">gzip</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">GA4GH Beacon</xref> + </xrefs> + </xml> + <xml name="creators"> + <creator> + <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" /> + <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" /> + <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" /> + <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" /> + <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" /> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btac568</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/Beacon-v2-Models_template.xlsx |
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| Binary file test-data/Beacon-v2-Models_template.xlsx has changed |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572721.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572721.json Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007500", + "subject": { + "id": "P0007500", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:37:19.994Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007500", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007500", + "subject": { + "id": "P0007500", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:37:19.994Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572724.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572724.json Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007499", + "subject": { + "id": "P0007499", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:33:50.417Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007499", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007499", + "subject": { + "id": "P0007499", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:33:50.417Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572727.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572727.json Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,268 @@ +{ + "phenopacket": { + "id": "P0007498", + "subject": { + "id": "P0007498", + "dateOfBirth": "2013-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0001249", + "label": "Intellectual disability" + } + }, + { + "type": { + "id": "HP:0000467", + "label": "Neck muscle weakness" + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Muscular hypotonia" + } + }, + { + "type": { + "id": "HP:0001319", + "label": "Neonatal hypotonia" + } + }, + { + "type": { + "id": "HP:0001374", + "label": "Congenital hip dislocation" + } + }, + { + "type": { + "id": "HP:0002540", + "label": "Inability to walk" + } + }, + { + "type": { + "id": "HP:0002783", + "label": "Recurrent lower respiratory tract infections" + } + }, + { + "type": { + "id": "HP:0002804", + "label": "Arthrogryposis multiplex congenita" + } + }, + { + "type": { + "id": "HP:0003202", + "label": "Skeletal muscle atrophy" + } + }, + { + "type": { + "id": "HP:0005684", + "label": "Distal arthrogryposis" + } + }, + { + "type": { + "id": "HP:0030319", + "label": "Weakness of facial musculature" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:97245", + "label": "Congenital myopathy" + } + }, + { + "term": { + "id": "OMIM:117000", + "label": "CENTRAL CORE DISEASE OF MUSCLE" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:32:38.488Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007498", + "resolutionStatus": "SOLVED", + "phenopacket": { + "id": "P0007498", + "subject": { + "id": "P0007498", + "dateOfBirth": "2013-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0001249", + "label": "Intellectual disability" + } + }, + { + "type": { + "id": "HP:0000467", + "label": "Neck muscle weakness" + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Muscular hypotonia" + } + }, + { + "type": { + "id": "HP:0001319", + "label": "Neonatal hypotonia" + } + }, + { + "type": { + "id": "HP:0001374", + "label": "Congenital hip dislocation" + } + }, + { + "type": { + "id": "HP:0002540", + "label": "Inability to walk" + } + }, + { + "type": { + "id": "HP:0002783", + "label": "Recurrent lower respiratory tract infections" + } + }, + { + "type": { + "id": "HP:0002804", + "label": "Arthrogryposis multiplex congenita" + } + }, + { + "type": { + "id": "HP:0003202", + "label": "Skeletal muscle atrophy" + } + }, + { + "type": { + "id": "HP:0005684", + "label": "Distal arthrogryposis" + } + }, + { + "type": { + "id": "HP:0030319", + "label": "Weakness of facial musculature" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:97245", + "label": "Congenital myopathy" + } + }, + { + "term": { + "id": "OMIM:117000", + "label": "CENTRAL CORE DISEASE OF MUSCLE" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:32:38.488Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572747.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572747.json Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,144 @@ +{ + "phenopacket": { + "id": "P0007501", + "subject": { + "id": "P0007501", + "dateOfBirth": "1980-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0007663", + "label": "Reduced visual acuity" + } + }, + { + "type": { + "id": "HP:0007703", + "label": "Abnormality of retinal pigmentation" + } + }, + { + "type": { + "id": "HP:0007722", + "label": "Retinal pigment epithelial atrophy" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:38:19.980Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007501", + "resolutionStatus": "SOLVED", + "phenopacket": { + "id": "P0007501", + "subject": { + "id": "P0007501", + "dateOfBirth": "1980-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0007663", + "label": "Reduced visual acuity" + } + }, + { + "type": { + "id": "HP:0007703", + "label": "Abnormality of retinal pigmentation" + } + }, + { + "type": { + "id": "HP:0007722", + "label": "Retinal pigment epithelial atrophy" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:38:19.980Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572750.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572750.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007502", + "subject": { + "id": "P0007502", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:38:48.402Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007502", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007502", + "subject": { + "id": "P0007502", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:38:48.402Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572753.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572753.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,168 @@ +{ + "phenopacket": { + "id": "P0007503", + "subject": { + "id": "P0007503", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000529", + "label": "Progressive visual loss" + } + }, + { + "type": { + "id": "HP:0000575", + "label": "Scotoma" + } + }, + { + "type": { + "id": "HP:0007703", + "label": "Abnormality of retinal pigmentation" + } + }, + { + "type": { + "id": "HP:0008002", + "label": "Abnormality of macular pigmentation" + } + }, + { + "type": { + "id": "HP:0012508", + "label": "Metamorphopsia" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:39:45.571Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007503", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007503", + "subject": { + "id": "P0007503", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000529", + "label": "Progressive visual loss" + } + }, + { + "type": { + "id": "HP:0000575", + "label": "Scotoma" + } + }, + { + "type": { + "id": "HP:0007703", + "label": "Abnormality of retinal pigmentation" + } + }, + { + "type": { + "id": "HP:0008002", + "label": "Abnormality of macular pigmentation" + } + }, + { + "type": { + "id": "HP:0012508", + "label": "Metamorphopsia" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:39:45.571Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572756.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572756.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007505", + "subject": { + "id": "P0007505", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:40:55.665Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007505", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007505", + "subject": { + "id": "P0007505", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:40:55.665Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572759.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572759.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007506", + "subject": { + "id": "P0007506", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:41:40.867Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007506", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007506", + "subject": { + "id": "P0007506", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:41:40.867Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572762.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572762.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,170 @@ +{ + "phenopacket": { + "id": "P0007504", + "subject": { + "id": "P0007504", + "dateOfBirth": "2002-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0003236", + "label": "Elevated serum creatine phosphokinase" + } + }, + { + "type": { + "id": "HP:0001324", + "label": "Muscle weakness" + } + }, + { + "type": { + "id": "HP:0003326", + "label": "Myalgia" + } + }, + { + "type": { + "id": "HP:0003560", + "label": "Muscular dystrophy" + } + }, + { + "type": { + "id": "HP:0009050", + "label": "Quadriceps muscle atrophy" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:40:31.348Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007504", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007504", + "subject": { + "id": "P0007504", + "dateOfBirth": "2002-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0003236", + "label": "Elevated serum creatine phosphokinase" + } + }, + { + "type": { + "id": "HP:0001324", + "label": "Muscle weakness" + } + }, + { + "type": { + "id": "HP:0003326", + "label": "Myalgia" + } + }, + { + "type": { + "id": "HP:0003560", + "label": "Muscular dystrophy" + } + }, + { + "type": { + "id": "HP:0009050", + "label": "Quadriceps muscle atrophy" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:40:31.348Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572861.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572861.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| b'@@ -0,0 +1,348 @@\n+{\n+ "phenopacket": {\n+ "id": "P0007507",\n+ "subject": {\n+ "id": "P0007507",\n+ "dateOfBirth": "2012-01-01T00:00:00Z",\n+ "sex": "MALE"\n+ },\n+ "phenotypicFeatures": [\n+ {\n+ "negated": true,\n+ "type": {\n+ "id": "HP:0007281",\n+ "label": "Developmental stagnation"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0000252",\n+ "label": "Microcephaly"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0001250",\n+ "label": "Seizures"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0001270",\n+ "label": "Motor delay"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002013",\n+ "label": "Vomiting"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002240",\n+ "label": "Hepatomegaly"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002333",\n+ "label": "Motor deterioration"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002376",\n+ "label": "Developmental regression"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002490",\n+ "label": "Increased CSF lactate"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002922",\n+ "label": "Increased CSF protein"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003128",\n+ "label": "Lactic acidosis"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003390",\n+ "label": "Sensory axonal neuropathy"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003739",\n+ "label": "Myoclonic spasms"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0004325",\n+ "label": "Decreased body weight"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0006887",\n+ "label": "Intellectual disability, progressive"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0007002",\n+ "label": "Motor axonal neuropathy"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0012758",\n+ "label": "Neurodevelopmental delay"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0100543",\n+ "label": "Cognitive impairment"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0200134",\n+ "label": "Epileptic encephalopathy"\n+ }\n+ }\n+ ],\n+ "diseases": [],\n+ "genes": [\n+ {\n+ "id": "HGNC:",\n+ "symbol": "OPA1"\n+ }\n+ ],\n+ "variants": [],\n+ "meta_data": {\n+ "created": "2021-04-21T09:42:24.702Z",\n+ "resources": [\n+ {\n+ "id": "hp",\n+ "name": "Human Phenotype Ontology",\n+ "url": "http://purl.obolibrary.org/obo/hp.owl",\n+ "version": "2020-12-07",\n+ "namespacePrefix": "HP",\n+ "iriPrefix": "http://purl.obolibrary.org/obo/HP_"\n+ },\n+ {\n+ "id": "orphanet",\n+ "name": "Orphanet Rare Disease Ontology",\n+ "url": "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version": "3.1",\n+ "namespacePrefix": "Orphanet",\n+ "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_"\n+ },\n+ {\n+ "id": "hgnc",\n+ "name": "HUGO Gene Nomenclature Committee",\n+ "url": "https://www.genenames.org",\n+ "version": "2021-01-13",\n+ "namespacePrefix": "HGNC",\n+ "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"\n+ },\n+ {\n+ "id": "mim",\n+ "name": "Online Mendelian Inheritance in Man",\n+ "url": "https://omim.org/",\n+ "version": "2021-01-21",\n+ "namespacePrefix": "OMIM",\n+ "iriPrefix": "https://omim.org/entry/"\n+ }\n+ ]\n+ }\n+ },\n+ "interpretation": {\n+ '..b'+ {\n+ "type": {\n+ "id": "HP:0000252",\n+ "label": "Microcephaly"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0001250",\n+ "label": "Seizures"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0001270",\n+ "label": "Motor delay"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002013",\n+ "label": "Vomiting"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002240",\n+ "label": "Hepatomegaly"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002333",\n+ "label": "Motor deterioration"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002376",\n+ "label": "Developmental regression"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002490",\n+ "label": "Increased CSF lactate"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0002922",\n+ "label": "Increased CSF protein"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003128",\n+ "label": "Lactic acidosis"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003390",\n+ "label": "Sensory axonal neuropathy"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0003739",\n+ "label": "Myoclonic spasms"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0004325",\n+ "label": "Decreased body weight"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0006887",\n+ "label": "Intellectual disability, progressive"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0007002",\n+ "label": "Motor axonal neuropathy"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0012758",\n+ "label": "Neurodevelopmental delay"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0100543",\n+ "label": "Cognitive impairment"\n+ }\n+ },\n+ {\n+ "type": {\n+ "id": "HP:0200134",\n+ "label": "Epileptic encephalopathy"\n+ }\n+ }\n+ ],\n+ "diseases": [],\n+ "genes": [\n+ {\n+ "id": "HGNC:",\n+ "symbol": "OPA1"\n+ }\n+ ],\n+ "variants": [],\n+ "meta_data": {\n+ "created": "2021-04-21T09:42:24.702Z",\n+ "resources": [\n+ {\n+ "id": "hp",\n+ "name": "Human Phenotype Ontology",\n+ "url": "http://purl.obolibrary.org/obo/hp.owl",\n+ "version": "2020-12-07",\n+ "namespacePrefix": "HP",\n+ "iriPrefix": "http://purl.obolibrary.org/obo/HP_"\n+ },\n+ {\n+ "id": "orphanet",\n+ "name": "Orphanet Rare Disease Ontology",\n+ "url": "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version": "3.1",\n+ "namespacePrefix": "Orphanet",\n+ "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_"\n+ },\n+ {\n+ "id": "hgnc",\n+ "name": "HUGO Gene Nomenclature Committee",\n+ "url": "https://www.genenames.org",\n+ "version": "2021-01-13",\n+ "namespacePrefix": "HGNC",\n+ "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"\n+ },\n+ {\n+ "id": "mim",\n+ "name": "Online Mendelian Inheritance in Man",\n+ "url": "https://omim.org/",\n+ "version": "2021-01-21",\n+ "namespacePrefix": "OMIM",\n+ "iriPrefix": "https://omim.org/entry/"\n+ }\n+ ]\n+ }\n+ },\n+ "diagnosis": [],\n+ "meta_data": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572881.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572881.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007508", + "subject": { + "id": "P0007508", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:42:56.635Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007508", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007508", + "subject": { + "id": "P0007508", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:42:56.635Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572884.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572884.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0007509", + "subject": { + "id": "P0007509", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:43:53.656Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0007509", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0007509", + "subject": { + "id": "P0007509", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:43:53.656Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572887.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572887.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,174 @@ +{ + "phenopacket": { + "id": "P0008909", + "subject": { + "id": "P0008909", + "dateOfBirth": "1982-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0000144", + "label": "Decreased fertility" + } + }, + { + "negated": true, + "type": { + "id": "HP:0003003", + "label": "Colon cancer" + } + }, + { + "type": { + "id": "HP:0003002", + "label": "Breast carcinoma" + } + }, + { + "type": { + "id": "HP:0100013", + "label": "Neoplasm of the breast" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:145", + "label": "Hereditary breast and ovarian cancer syndrome" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:45:31.121Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0008909", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0008909", + "subject": { + "id": "P0008909", + "dateOfBirth": "1982-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "negated": true, + "type": { + "id": "HP:0000144", + "label": "Decreased fertility" + } + }, + { + "negated": true, + "type": { + "id": "HP:0003003", + "label": "Colon cancer" + } + }, + { + "type": { + "id": "HP:0003002", + "label": "Breast carcinoma" + } + }, + { + "type": { + "id": "HP:0100013", + "label": "Neoplasm of the breast" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:145", + "label": "Hereditary breast and ovarian cancer syndrome" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:45:31.121Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572890.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572890.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,120 @@ +{ + "phenopacket": { + "id": "P0008910", + "subject": { + "id": "P0008910", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0100615", + "label": "Ovarian neoplasm" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:48:57.456Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0008910", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0008910", + "subject": { + "id": "P0008910", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0100615", + "label": "Ovarian neoplasm" + } + } + ], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:48:57.456Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572893.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572893.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0008911", + "subject": { + "id": "P0008911", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:47:54.584Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0008911", + "resolutionStatus": "UNKNOWN", + "phenopacket": { + "id": "P0008911", + "subject": { + "id": "P0008911", + "dateOfBirth": "unknown-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:47:54.584Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572896.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572896.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,182 @@ +{ + "phenopacket": { + "id": "P0130406", + "subject": { + "id": "P0130406", + "dateOfBirth": "2019-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000467", + "label": "Neck muscle weakness" + } + }, + { + "type": { + "id": "HP:0005684", + "label": "Distal arthrogryposis" + } + }, + { + "type": { + "id": "HP:0008936", + "label": "Muscular hypotonia of the trunk" + } + }, + { + "type": { + "id": "HP:0003202", + "label": "Skeletal muscle atrophy" + } + }, + { + "type": { + "id": "HP:0001319", + "label": "Neonatal hypotonia" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:97245", + "label": "Congenital myopathy" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:50:13.849Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0130406", + "resolutionStatus": "UNSOLVED", + "phenopacket": { + "id": "P0130406", + "subject": { + "id": "P0130406", + "dateOfBirth": "2019-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000467", + "label": "Neck muscle weakness" + } + }, + { + "type": { + "id": "HP:0005684", + "label": "Distal arthrogryposis" + } + }, + { + "type": { + "id": "HP:0008936", + "label": "Muscular hypotonia of the trunk" + } + }, + { + "type": { + "id": "HP:0003202", + "label": "Skeletal muscle atrophy" + } + }, + { + "type": { + "id": "HP:0001319", + "label": "Neonatal hypotonia" + } + } + ], + "diseases": [ + { + "term": { + "id": "Orphanet:97245", + "label": "Congenital myopathy" + } + } + ], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:50:13.849Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572899.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572899.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0669040", + "subject": { + "id": "P0669040", + "dateOfBirth": "1986-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:52:45.533Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0669040", + "resolutionStatus": "UNKNOWN", + "phenopacket": { + "id": "P0669040", + "subject": { + "id": "P0669040", + "dateOfBirth": "1986-01-01T00:00:00Z", + "sex": "FEMALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:52:45.533Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/EGAF00005572902.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EGAF00005572902.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,106 @@ +{ + "phenopacket": { + "id": "P0244875", + "subject": { + "id": "P0244875", + "dateOfBirth": "1987-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:51:14.643Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "interpretation": { + "id": "P0244875", + "resolutionStatus": "UNKNOWN", + "phenopacket": { + "id": "P0244875", + "subject": { + "id": "P0244875", + "dateOfBirth": "1987-01-01T00:00:00Z", + "sex": "MALE" + }, + "phenotypicFeatures": [], + "diseases": [], + "genes": [], + "variants": [], + "meta_data": { + "created": "2021-04-21T09:51:14.643Z", + "resources": [ + { + "id": "hp", + "name": "Human Phenotype Ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2020-12-07", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + }, + { + "id": "orphanet", + "name": "Orphanet Rare Disease Ontology", + "url": "http://orpha.net/ontology/ORDO_en_3.1.owl", + "version": "3.1", + "namespacePrefix": "Orphanet", + "iriPrefix": "http://www.orpha.net/ORDO/Orphanet_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "2021-01-13", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "mim", + "name": "Online Mendelian Inheritance in Man", + "url": "https://omim.org/", + "version": "2021-01-21", + "namespacePrefix": "OMIM", + "iriPrefix": "https://omim.org/entry/" + } + ] + } + }, + "diagnosis": [], + "meta_data": {} + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/analyses.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/analyses.csv Sun Oct 01 16:30:46 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +aligner,analysisDate,biosampleId,id,individualId,pipelineName,pipelineRef,runId,variantCaller |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/bff_validation.text --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bff_validation.text Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,20 @@ +[1m[36m**************************************** +* Beacon v2 Reference Implementation * +* - BEACON FRIENDLY FORMAT VALIDATOR - * +* Version: 2.0.0 * +* (C) 2021-2022 Manuel Rueda, PhD * +* GNU General Public License v3 * +**************************************** + +[1m[34m==== SCHEMA: ANALYSES ====[0m +[1m[32mHurray! No errors found[0m +[1m[34m==== SCHEMA: BIOSAMPLES ====[0m +[1m[32mHurray! No errors found[0m +[1m[34m==== SCHEMA: COHORTS ====[0m +[1m[32mHurray! No errors found[0m +[1m[34m==== SCHEMA: DATASETS ====[0m +[1m[32mHurray! No errors found[0m +[1m[34m==== SCHEMA: INDIVIDUALS ====[0m +[1m[32mHurray! No errors found[0m +[1m[34m==== SCHEMA: RUNS ====[0m +[1m[32mHurray! No errors found[0m |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/biosamples.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosamples.csv Sun Oct 01 16:30:46 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +biosampleStatus.id,biosampleStatus.label,collectionDate,collectionMoment,diagnosticMarkers_id,diagnosticMarkers_label,histologicalDiagnosis.id,histologicalDiagnosis.label,id,individualId,measurements_assayCode.id,measurements_assayCode.label,measurements_date,measurements_measurementValue,measurements_notes,measurements_observationMoment,measurements_procedure.ageAtProcedure,measurements_procedure.bodySite.id,measurements_procedure.bodySite.label,measurements_procedure.dateOfProcedure,measurements_procedure.procedureCode.id,measurements_procedure.procedureCode.label,notes,obtentionProcedure.ageAtProcedure,obtentionProcedure.bodySite.id,obtentionProcedure.bodySite.label,obtentionProcedure.dateOfProcedure,obtentionProcedure.procedureCode.id,obtentionProcedure.procedureCode.label,pathologicalStage.id,pathologicalStage.label,pathologicalTnmFinding_id,pathologicalTnmFinding_label,phenotypicFeatures_evidence.evidenceCode.id,phenotypicFeatures_evidence.evidenceCode.label,phenotypicFeatures_evidence.reference.id,phenotypicFeatures_evidence.reference.notes,phenotypicFeatures_evidence.reference.reference,phenotypicFeatures_excluded,phenotypicFeatures_featureType.id,phenotypicFeatures_featureType.label,phenotypicFeatures_modifiers,phenotypicFeatures_notes,phenotypicFeatures_onset,phenotypicFeatures_resolution,phenotypicFeatures_severity.id,phenotypicFeatures_severity.label,sampleOriginDetail.id,sampleOriginDetail.label,sampleOriginType.id,sampleOriginType.label,sampleProcessing.id,sampleProcessing.label,sampleStorage.id,sampleStorage.label,tumorGrade.id,tumorGrade.label,tumorProgression.id,tumorProgression.label |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/cohorts.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cohorts.csv Sun Oct 01 16:30:46 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +cohortDataTypes_id,cohortDataTypes_label,cohortDesign.id,cohortDesign.label,cohortSize,cohortType,collectionEvents_eventAgeRange.availability,collectionEvents_eventAgeRange.availabilityCount,collectionEvents_eventAgeRange.distribution,collectionEvents_eventCases,collectionEvents_eventControls,collectionEvents_eventDataTypes.availability,collectionEvents_eventDataTypes.availabilityCount,collectionEvents_eventDataTypes.distribution,collectionEvents_eventDate,collectionEvents_eventDiseases.availability,collectionEvents_eventDiseases.availabilityCount,collectionEvents_eventDiseases.distribution,collectionEvents_eventEthnicities.availability,collectionEvents_eventEthnicities.availabilityCount,collectionEvents_eventEthnicities.distribution,collectionEvents_eventGenders.availability,collectionEvents_eventGenders.availabilityCount,collectionEvents_eventGenders.distribution,collectionEvents_eventLocations.availability,collectionEvents_eventLocations.availabilityCount,collectionEvents_eventLocations.distribution,collectionEvents_eventNum,collectionEvents_eventPhenotypes.availability,collectionEvents_eventPhenotypes.availabilityCount,collectionEvents_eventPhenotypes.distribution,collectionEvents_eventSize,collectionEvents_eventTimeline.end,collectionEvents_eventTimeline.start,exclusionCriteria.ageRange.end.iso8601duration,exclusionCriteria.ageRange.start.iso8601duration,exclusionCriteria.diseaseConditions,exclusionCriteria.ethnicities,exclusionCriteria.genders,exclusionCriteria.locations,exclusionCriteria.phenotypicConditions,id,inclusionCriteria.ageRange.end.iso8601duration,inclusionCriteria.ageRange.start.iso8601duration,inclusionCriteria.diseaseConditions,inclusionCriteria.ethnicities,inclusionCriteria.genders,inclusionCriteria.locations,inclusionCriteria.phenotypicConditions,name,ids.individualIds,ids.biosampleIds |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/datasets.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datasets.csv Sun Oct 01 16:30:46 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +createDateTime,dataUseConditions.duoDataUse,description,externalUrl,id,name,updateDateTime,version,ids.individualIds,ids.biosampleIds |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/genomicVariations.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genomicVariations.csv Sun Oct 01 16:30:46 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +caseLevelData_alleleOrigin.id,caseLevelData_alleleOrigin.label,caseLevelData_analysisId,caseLevelData_biosampleId,caseLevelData_clinicalInterpretations,caseLevelData_id,caseLevelData_individualId,caseLevelData_phenotypicEffects,caseLevelData_runId,caseLevelData_zygosity.id,caseLevelData_zygosity.label,frequencyInPopulations_frequencies,frequencyInPopulations_source,frequencyInPopulations_sourceReference,frequencyInPopulations_version,identifiers.clinvarVariantId,identifiers.genomicHGVSId,identifiers.proteinHGVSIds,identifiers.transcriptHGVSIds,identifiers.variantAlternativeIds,molecularAttributes.aminoacidChanges,molecularAttributes.geneIds,molecularAttributes.genomicFeatures,molecularAttributes.molecularEffects,variantInternalId,variantLevelData.clinicalInterpretations,variantLevelData.phenotypicEffects,variation |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/genomicVariationsVcf.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genomicVariationsVcf.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| b'@@ -0,0 +1,37 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| diff -r 000000000000 -r ba4ed464f8b6 test-data/individuals.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/individuals.csv Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,1 @@ +diseases_ageOfOnset,diseases_diseaseCode.id,diseases_diseaseCode.label,diseases_familyHistory,diseases_notes,diseases_severity.id,diseases_severity.label,diseases_stage.id,diseases_stage.label,ethnicity.id,ethnicity.label,exposures_ageAtExposure.iso8601duration,exposures_date,exposures_duration,exposures_exposureCode.id,exposures_exposureCode.label,exposures_unit.id,exposures_unit.label,exposures_value,geographicOrigin.id,geographicOrigin.label,id,interventionsOrProcedures_ageAtProcedure,interventionsOrProcedures_bodySite.id,interventionsOrProcedures_bodySite.label,interventionsOrProcedures_dateOfProcedure,interventionsOrProcedures_procedureCode.id,interventionsOrProcedures_procedureCode.label,karyotypicSex,measures_assayCode.id,measures_assayCode.label,measures_date,measures_measurementValue,measures_notes,measures_observationMoment,measures_procedure.ageAtProcedure,measures_procedure.bodySite.id,measures_procedure.bodySite.label,measures_procedure.dateOfProcedure,measures_procedure.procedureCode.id,measures_procedure.procedureCode.label,pedigrees_disease.ageOfOnset,pedigrees_disease.diseaseCode.id,pedigrees_disease.diseaseCode.label,pedigrees_disease.familyHistory,pedigrees_disease.notes,pedigrees_disease.severity.id,pedigrees_disease.severity.label,pedigrees_disease.stage.id,pedigrees_disease.stage.label,pedigrees_id,pedigrees_members,pedigrees_numSubjects,phenotypicFeatures_evidence.evidenceCode.id,phenotypicFeatures_evidence.evidenceCode.label,phenotypicFeatures_evidence.reference.id,phenotypicFeatures_evidence.reference.notes,phenotypicFeatures_evidence.reference.reference,phenotypicFeatures_excluded,phenotypicFeatures_featureType.id,phenotypicFeatures_featureType.label,phenotypicFeatures_modifiers,phenotypicFeatures_notes,phenotypicFeatures_onset,phenotypicFeatures_resolution,phenotypicFeatures_severity.id,phenotypicFeatures_severity.label,sex.id,sex.label,treatments_ageAtOnset.iso8601duration,treatments_cumulativeDose.referenceRange.high,treatments_cumulativeDose.referenceRange.low,treatments_cumulativeDose.referenceRange.unit,treatments_cumulativeDose.unit.id,treatments_cumulativeDose.unit.label,treatments_cumulativeDose.value,treatments_doseIntervals,treatments_routeOfAdministration.id,treatments_routeOfAdministration.label,treatments_treatmentCode.id,treatments_treatmentCode.label |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/individuals.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/individuals.json Sun Oct 01 16:30:46 2023 +0000 |
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| b'@@ -0,0 +1,2141 @@\n+[\n+ {\n+ "diseases" : [],\n+ "id" : "P0007502",\n+ "info" : {\n+ "interpretation" : {\n+ "diagnosis" : [],\n+ "phenopacket" : {\n+ "meta_data" : {\n+ "created" : "2021-04-21T09:38:48.402Z",\n+ "resources" : [\n+ {\n+ "id" : "hp",\n+ "iriPrefix" : "http://purl.obolibrary.org/obo/HP_",\n+ "name" : "Human Phenotype Ontology",\n+ "namespacePrefix" : "HP",\n+ "url" : "http://purl.obolibrary.org/obo/hp.owl",\n+ "version" : "2020-12-07"\n+ },\n+ {\n+ "id" : "orphanet",\n+ "iriPrefix" : "http://www.orpha.net/ORDO/Orphanet_",\n+ "name" : "Orphanet Rare Disease Ontology",\n+ "namespacePrefix" : "Orphanet",\n+ "url" : "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version" : "3.1"\n+ },\n+ {\n+ "id" : "hgnc",\n+ "iriPrefix" : "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",\n+ "name" : "HUGO Gene Nomenclature Committee",\n+ "namespacePrefix" : "HGNC",\n+ "url" : "https://www.genenames.org",\n+ "version" : "2021-01-13"\n+ },\n+ {\n+ "id" : "mim",\n+ "iriPrefix" : "https://omim.org/entry/",\n+ "name" : "Online Mendelian Inheritance in Man",\n+ "namespacePrefix" : "OMIM",\n+ "url" : "https://omim.org/",\n+ "version" : "2021-01-21"\n+ }\n+ ]\n+ }\n+ },\n+ "resolutionStatus" : "UNSOLVED"\n+ },\n+ "phenopacket" : {\n+ "dateOfBirth" : "unknown-01-01T00:00:00Z",\n+ "genes" : [],\n+ "meta_data" : {\n+ "created" : "2021-04-21T09:38:48.402Z",\n+ "resources" : [\n+ {\n+ "id" : "hp",\n+ "iriPrefix" : "http://purl.obolibrary.org/obo/HP_",\n+ "name" : "Human Phenotype Ontology",\n+ "namespacePrefix" : "HP",\n+ "url" : "http://purl.obolibrary.org/obo/hp.owl",\n+ "version" : "2020-12-07"\n+ },\n+ {\n+ "id" : "orphanet",\n+ "iriPrefix" : "http://www.orpha.net/ORDO/Orphanet_",\n+ "name" : "Orphanet Rare Disease Ontology",\n+ "namespacePrefix" : "Orphanet",\n+ "url" : "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version" : "3.1"\n+ },\n+ {\n+ "id" : "hgnc",\n+ "iriPrefix" : "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",\n+ "name" : "HUGO Gene Nomenclature Committee",\n+ "namespacePrefix" : "HGNC",\n+ "url" : "https://www.genenames.org",\n+ "version" : "2021-01-13"\n+ },\n+ {\n+ "id" : "mim",\n+ "iriPrefix" : "https://omim.org/entry/",\n+ "name" : "Online Mendelian Inheritance in Man",\n+ "namespacePrefix" : "OMIM",\n+ "url" : "https://omim.org/",\n+ "version" : "2021-01-21"\n+ }\n+ ]\n+ },\n+ "variants" : []\n+ }\n+ },\n+ "phenotypicFeatures" : [],\n+ "sex" : {\n+ "id" : "NCIT:C20197",\n+ "la'..b'.owl",\n+ "version" : "2020-12-07"\n+ },\n+ {\n+ "id" : "orphanet",\n+ "iriPrefix" : "http://www.orpha.net/ORDO/Orphanet_",\n+ "name" : "Orphanet Rare Disease Ontology",\n+ "namespacePrefix" : "Orphanet",\n+ "url" : "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version" : "3.1"\n+ },\n+ {\n+ "id" : "hgnc",\n+ "iriPrefix" : "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",\n+ "name" : "HUGO Gene Nomenclature Committee",\n+ "namespacePrefix" : "HGNC",\n+ "url" : "https://www.genenames.org",\n+ "version" : "2021-01-13"\n+ },\n+ {\n+ "id" : "mim",\n+ "iriPrefix" : "https://omim.org/entry/",\n+ "name" : "Online Mendelian Inheritance in Man",\n+ "namespacePrefix" : "OMIM",\n+ "url" : "https://omim.org/",\n+ "version" : "2021-01-21"\n+ }\n+ ]\n+ }\n+ },\n+ "resolutionStatus" : "SOLVED"\n+ },\n+ "phenopacket" : {\n+ "dateOfBirth" : "1980-01-01T00:00:00Z",\n+ "genes" : [],\n+ "meta_data" : {\n+ "created" : "2021-04-21T09:38:19.980Z",\n+ "resources" : [\n+ {\n+ "id" : "hp",\n+ "iriPrefix" : "http://purl.obolibrary.org/obo/HP_",\n+ "name" : "Human Phenotype Ontology",\n+ "namespacePrefix" : "HP",\n+ "url" : "http://purl.obolibrary.org/obo/hp.owl",\n+ "version" : "2020-12-07"\n+ },\n+ {\n+ "id" : "orphanet",\n+ "iriPrefix" : "http://www.orpha.net/ORDO/Orphanet_",\n+ "name" : "Orphanet Rare Disease Ontology",\n+ "namespacePrefix" : "Orphanet",\n+ "url" : "http://orpha.net/ontology/ORDO_en_3.1.owl",\n+ "version" : "3.1"\n+ },\n+ {\n+ "id" : "hgnc",\n+ "iriPrefix" : "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",\n+ "name" : "HUGO Gene Nomenclature Committee",\n+ "namespacePrefix" : "HGNC",\n+ "url" : "https://www.genenames.org",\n+ "version" : "2021-01-13"\n+ },\n+ {\n+ "id" : "mim",\n+ "iriPrefix" : "https://omim.org/entry/",\n+ "name" : "Online Mendelian Inheritance in Man",\n+ "namespacePrefix" : "OMIM",\n+ "url" : "https://omim.org/",\n+ "version" : "2021-01-21"\n+ }\n+ ]\n+ },\n+ "variants" : []\n+ }\n+ },\n+ "phenotypicFeatures" : [\n+ {\n+ "excluded" : false,\n+ "featureType" : {\n+ "id" : "HP:0007663",\n+ "label" : "Reduced visual acuity"\n+ }\n+ },\n+ {\n+ "excluded" : false,\n+ "featureType" : {\n+ "id" : "HP:0007703",\n+ "label" : "Abnormality of retinal pigmentation"\n+ }\n+ },\n+ {\n+ "excluded" : false,\n+ "featureType" : {\n+ "id" : "HP:0007722",\n+ "label" : "Retinal pigment epithelial atrophy"\n+ }\n+ }\n+ ],\n+ "sex" : {\n+ "id" : "NCIT:C20197",\n+ "label" : "male"\n+ }\n+ }\n+]\n' |
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| diff -r 000000000000 -r ba4ed464f8b6 test-data/merge_output_1.vcf.gz |
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| Binary file test-data/merge_output_1.vcf.gz has changed |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/runs.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/runs.csv Sun Oct 01 16:30:46 2023 +0000 |
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| @@ -0,0 +1,1 @@ +biosampleId,id,individualId,libraryLayout,librarySelection,librarySource.id,librarySource.label,libraryStrategy,platform,platformModel.id,platformModel.label,runDate |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/runs.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/runs.json Sun Oct 01 16:30:46 2023 +0000 |
| [ |
| @@ -0,0 +1,56 @@ +[ + { + "biosampleId": "S0001", + "id": "INT_ID1", + "individualId": "NA24631", + "libraryLayout": "PAIRED", + "librarySelection": "LD-PCR", + "librarySource": { + "id": "NNN:01", + "label": "KAPA library quantification kit" + }, + "libraryStrategy": "WGS", + "platform": "Illumina ", + "runDate": "2017-04-30", + "platformModel": { + "id": "MODEL:HiSeq 2500 ", + "label": "2017-04-30" + } + }, + { + "biosampleId": "S0002", + "id": "INT_ID2", + "individualId": "NA24694", + "libraryLayout": "PAIRED", + "librarySelection": "LD-PCR", + "librarySource": { + "id": "NNN:01", + "label": "KAPA library quantification kit" + }, + "libraryStrategy": "WGS", + "platform": "Illumina ", + "runDate": "2017-04-30", + "platformModel": { + "id": "MODEL:HiSeq 2500 ", + "label": "2017-04-30" + } + }, + { + "biosampleId": "S0003", + "id": "INT_ID3", + "individualId": "NA24695", + "libraryLayout": "PAIRED", + "runDate": "2017-04-30", + "librarySelection": "LD-PCR", + "librarySource": { + "id": "NNN:01", + "label": "KAPA library quantification kit" + }, + "libraryStrategy": "WGS", + "platform": "Illumina ", + "platformModel": { + "id": "MODEL:HiSeq 2500 ", + "label": "2017-04-30" + } + } +] |
| b |
| diff -r 000000000000 -r ba4ed464f8b6 test-data/test.vcf.gz |
| b |
| Binary file test-data/test.vcf.gz has changed |