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, falsedescription (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, GVCFgenome_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, falseextra_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, Causativeextra_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_progressphenopacket (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