Phenopackets API

Data types endpoints

Phenotypic features

api/phenotypicfeatures GET: list of phenotypic features

api/phenotypicfeatures/{id} GET: single phenotypic feature

The following filters can be applied:

  • id (exact match, single): /api/phenotypicfeatures?id=112002

  • negated: /api/phenotypicfeatures?negated=false options: true, false

  • description (case-insensitive partial match): /api/phenotypicfeatures?description=test

  • type (case-insensitive partial match): /api/phenotypicfeatures?type=hypertension or /api/phenotypicfeatures?type=HP:0000822

  • severity (case-insensitive partial match): /api/phenotypicfeatures?severity=mild or /api/phenotypicfeatures?severity=HP:0012825

  • onset (case-insensitive partial match): /api/phenotypicfeatures?onset=adult or /api/phenotypicfeatures?onset=HP:0003581

  • evidence (case-insensitive partial match): /api/phenotypicfeatures?evidence=author statement or /api/phenotypicfeatures?evidence=ECO:0006017

  • extra_properties (case-insensitive partial match): /api/phenotypicfeatures?extra_properties=test

  • extra_properties_datatype (ONLY if “datatype” is present in extra_properties, case-insensitive partial match): /api/phenotypicfeatures?extra_properties_datatype=comorbidities

  • individual (single or multiple individuals ids separated by comma), returns all phenotypic features for listed individuals: /api/phenotypicfeatures?individual=10001,10002

  • biosample (single), returns phenotypic features that are related to a specified biosample: /api/phenotypicfeatures?biosample=2615-01

  • phenopacket (single), returns phenotypic features that are related to a specified phenopacket: /api/phenotypicfeatures?phenopacket=20110

  • datasets (single or multiple list of datasets titles separated by comma): /api/phenotypicfeatures?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/phenotypicfeatures?authorized_datasets=dataset_1,dataset_2

Procedures

api/procedures GET: list of phenotypic features

api/procedures/{id} GET: single phenotypic feature

The following filters can be applied:

  • id (exact match, single): /api/procedures?id=112002

  • code (case-insensitive partial match): /api/procedures?code=punch biopsy or /api/procedures?code=NCIT:C28743

  • body_site (case-insensitive partial match): /api/procedures?body_site=skin of forearm or /api/procedures?body_site=UBERON:0003403

  • biosample (single), returns procedure that was performed on a specified biosample: /api/procedures?biosample=2615-01

  • extra_properties (case-insensitive partial match): /api/procedures?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/procedures?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/procedures?authorized_datasets=dataset_1,dataset_2

HTS Files

api/htsfiles GET: list of HTS files

api/htsfiles/{uri} GET: single HTS files

The following filters can be applied:

  • uri (exact match, single): /api/htsfiles?uri=drs://data/10001.vcf.gz

  • description (case-insensitive partial match): /api/htsfiles?description=test

  • hts_format (case-insensitive exact match): /api/htsfiles?hts_format=VCF options: UNKNOWN, SAM, BAM, CRAM, VCF, BCF, GVCF

  • genome_assembly (case-insensitive exact match): /api/htsfiles?genome_assembly=GRCh37

  • extra_properties (case-insensitive partial match): /api/htsfiles?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/htsfiles?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/htsfiles?authorized_datasets=dataset_1,dataset_2

Genes

api/genes GET: list of Genes

api/genes/{id} GET: single Gene

The following filters can be applied:

  • id (single, exact match), takes an official identifier of the gene according to HGNC: /api/genes?id=HGNC:347

  • symbol (single, exact match), takes an official symbol of the gene according to HGNC: /api/genes?symbol=ETF1

  • extra_properties (case-insensitive partial match): /api/genes?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/genes?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/genes?authorized_datasets=dataset_1,dataset_2

Variants

api/variants GET: list of Variants

api/variants/{id} GET: single Variants

The following filters can be applied:

  • id (single, exact match): /api/variants?id=100

  • allele_type (single, case-insensitive exact match): /api/variants?allele_type=spdiAllele

  • zygosity (case-insensitive partial match): /api/variants?zygosity=heterozygous or /api/variants?zygosity=GENO:0000135

  • extra_properties (case-insensitive partial match): /api/variants?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/variants?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/variants?authorized_datasets=dataset_1,dataset_2

Diseases

api/diseases GET: list of Diseases

api/diseases/{id} GET: single Disease

The following filters can be applied:

  • id (single, exact match), disease id in Katsu database: /api/diseases?id=1

  • term (case-insensitive partial match): /api/diseases?term=COVID-19 or /api/diseases?term=SNOMED:840539006

  • extra_properties (case-insensitive partial match): /api/diseases?extra_properties=test

  • extra_properties_datatype (ONLY if “datatype” is present in extra_properties, case-insensitive partial match): /api/diseases?extra_properties_datatype=comorbidities

  • extra_properties_comorbidities_group (ONLY if “comorbidities_group” is present in extra_properties, case-insensitive partial match): /api/diseases?extra_properties_comorbidities_group=common

  • datasets (single or multiple list of datasets titles separated by comma): /api/diseases?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/diseases?authorized_datasets=dataset_1,dataset_2

Biosamples

api/biosamples GET: list of Biosamples

api/biosamples/{id} GET: single Biosample

The following filters can be applied:

  • id (single, exact match): /api/biosamples?id=1

  • description (case-insensitive partial match): /api/biosamples?description=test

  • sampled_tissue (case-insensitive partial match): /api/biosamples?sampled_tissue=urinary bladder or /api/biosamples?sampled_tissue=UBERON:0001256

  • taxonomy (case-insensitive partial match): /api/biosamples?taxonomy=homo sapiens or /api/biosamples?taxonomy=NCBITaxon:9606

  • histological_diagnosis (case-insensitive partial match): /api/biosamples?histological_diagnosis=negative finding or /api/biosamples?histological_diagnosis=NCIT:C38757

  • tumor_progression (case-insensitive partial match): /api/biosamples?tumor_progression=primary neoplasm or /api/biosamples?tumor_progression=NCIT:C8509

  • tumor_grade (case-insensitive partial match): /api/biosamples?tumor_grade=healed or /api/biosamples?tumor_grade=NCIT:C41133

  • individual (single, exact match, biosample must be related to Individual via ForeignKey not via Phenopacket): /api/biosamples?individual=10001

  • procedure (single, exact match, searches by procedure id): /api/biosamples?procedure=1

  • is_control_sample: /api/biosamples?is_control_sample=false options: true, false

  • extra_properties (case-insensitive partial match): /api/biosamples?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/biosamples?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/biosamples?authorized_datasets=dataset_1,dataset_2

Phenopackets

api/phenopackets GET: list of Phenopackets

api/phenopackets/{id} GET: single Phenopacket

The following filters can be applied:

  • id (single, exact match): /api/phenopackets?id=12000

  • subject (single, exact match), returns all phenopackets for a single individual: /api/phenopackets?subject=10001

  • disease (case-insensitive partial match): /api/phenopackets?disease=COVID-19 or /api/phenopackets?disease=SNOMED:840539006

  • found_phenotypic_feature (case-insensitive partial match): /api/phenopackets?found_phenotypic_feature=hypertension or /api/phenopackets?found_phenotypic_feature=HP:0000822

  • biosamples (single or multiple, exact match), takes biosample id, returns phenopacket(s) containing specified biosample(s): /api/phenopackets?biosamples=2231-20&biosamples=1289-21

  • genes (single or multiple, exact match), returns phenopacket(s) containing specified gene(s): /api/phenopackets?genes=HGNC:347

  • variants (single or multiple, exact match), returns phenopacket(s) containing specified variant(s): /api/phenopackets?variants=100&variants=101

  • hts_files (single or multiple, exact match), returns phenopacket(s) containing specified hts_file(s): /api/phenopackets?hts_files=drs://data/10001.vcf.gz&hts_files=drs://data/10002.vcf.gz

  • extra_properties (case-insensitive partial match): /api/phenopackets?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/phenopackets?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/phenopackets?authorized_datasets=dataset_1,dataset_2

Genomic Interpretations

api/genomicinterpretations GET: list of Genomic Interpretations

api/genomicinterpretations/{id} GET: single Genomic Interpretation

The following filters can be applied:

  • id (single, exact match): /api/genomicinterpretations?id=1

  • gene (single, exact match): /api/genomicinterpretations?gene=HGNC:347

  • variant (single, exact match): /api/genomicinterpretations?variant=100

  • status (case-insensitive, exact match): /api/genomicinterpretations?status=causative options: Unknown, Rejected, Candidate, Causative

  • extra_properties (case-insensitive partial match): /api/genomicinterpretations?extra_properties=test

Diagnoses

api/diagnoses GET: list of Diagnoses

api/diagnoses/{id} GET: single Diagnosis

The following filters can be applied:

  • id (single, exact match): /api/diagnoses?id=1

  • disease_type (case-insensitive partial match): /api/diagnoses?disease_type=COVID-19 or /api/diagnoses?disease_type=SNOMED:840539006

  • extra_properties (case-insensitive partial match): /api/diagnoses?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/diagnoses?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/diagnoses?authorized_datasets=dataset_1,dataset_2

Interpretations

api/interpretations GET: list of Interpretations

api/interpretations/{id} GET: single Interpretation

The following filters can be applied:

  • id (single, exact match): /api/interpretations?id=1

  • resolution_status (case-insensitive, exact match): /api/interpretations?resolution_status=causative options: Unknown, Solved, Unsolved, In_progress

  • phenopacket (single, exact match, searches by phenopacket id), returns all interpretations made for a specified phenopacket: /api/interpretations?phenopacket=12000

  • extra_properties (case-insensitive partial match): /api/interpretations?extra_properties=test

  • datasets (single or multiple list of datasets titles separated by comma): /api/interpretations?datasets=dataset_1,dataset_2

  • authorized_datasets (single or multiple list of authorized datasets titles separated by comma): /api/interpretations?authorized_datasets=dataset_1,dataset_2