API
Public API
The public API provides access to the public data stored in the Swiss Pathogen Surveillance Platform (SPSP). The data is organized in datasets, each containing different categories of samples. The public API allows users to browse the available data on SPSP.
Authentication
The public API does not require any authentication.
Endpoints
Base URL
The base URL of the public API is
https://spsp.sib.swiss/api/v1
The public API provides the following endpoints:
/datasets: list all datasets/{dataset}/{category}/last_update: get the last update of a category in a dataset/{dataset}/{category}/fields: list all fields of a given category in a dataset/{dataset}/{category}/samples: paginated list all samples of a given category in a dataset/{dataset}/{category}/submissions: list all submissions by week of a given category in a dataset/{dataset}/{category}/stats: get statistics of a given category in a dataset
GET /datasets
Description
Get the list of all datasets with their categories.
Try it out
https://spsp.sib.swiss/api/v1/datasets
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/datasets" -H "accept: application/json"
Example response
{
"viruses": [
"sars-cov-2",
"influenza",
"other"
],
"wastewater": [
"sars-cov-2"
]
}
GET /{dataset}/{category}/last_update
Description
Get the last update of a category in a dataset.
Try it out
https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/last_update
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/last_update" -H "accept: application/json"
Example response
{
"last_update": "2024-10-09"
}
GET /{dataset}/{category}/fields
Description
Get the list of all the available fields of a given category in a dataset.
Try it out
https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/fields
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/fields" -H "accept: application/json"
Example response
[
{
"id": 1,
"name": "ISOLATE.SPSP_identifier",
"is_public": true,
"type": "STRING",
"values": null
},
{
...
},
{
"id": 74,
"name": "FRAMESHIFTS.Frameshift_diagnosis",
"is_public": false,
"type": "BOOLEAN",
"values": null
}
]
GET /{dataset}/{category}/samples
Description
Get the paginated list of all samples of a given category in a dataset.
Try it out
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/samples?page=1&items-per-page=1&sort=-ISOLATE.SPSP_identifier" -H "accept: application/json"
Query parameters
page(integer): page number (required)items-per-page{field}(string): filter samples by field value (optional)sort-to sort in descending order)
Example response
{
"current_page": 1,
"last_page": 164600,
"from": 1,
"to": 1,
"total": 164600,
"data": [
{
"ISOLATE.SPSP_identifier": "SPSP155732",
"ISOLATE.Strain_name": "hCoV-19/Switzerland/AG-UZH-1000477914/2020",
"ISOLATE.Species_taxonomy_ID": 2697049,
"ISOLATE.Species_name": "SARS-CoV-2",
"ISOLATE.Genus": "Betacoronavirus",
"ISOLATE.Isolation_date": "2020-03-01",
"ISOLATE.Isolation_compartment": "HUMAN",
"ISOLATE.Isolation_site": false,
"ISOLATE.Isolation_location_-_continent": "EUROPE",
"ISOLATE.Isolation_location_-_country": "SWITZERLAND",
"ISOLATE.Isolation_location_-_division": "AG",
"ISOLATE.Isolation_location_-_ZIP": false,
"ISOLATE.Isolation_location_-_address": false,
"ISOLATE.Exposure_location_-_continent": true,
"ISOLATE.Exposure_location_-_country": true,
"ISOLATE.Exposure_location_-_division": true,
"ISOLATE.Reporting_lab_order_id": false,
"ISOLATE.Collecting_lab_order_id": false,
"ISOLATE.Collecting_lab_code": false,
"ISOLATE.Collecting_lab_name": "Department of Infectious Diseases, Cantonal Hospital Baden",
"HOST.Host_age": true,
"HOST.Host_sex": true,
"HOST.Host_clinical_status": false,
"SUBMISSION.Batch_name": false,
"SUBMISSION.Batch_submission_date": true,
"SUBMISSION.Reporting_lab_name": "Institute of Medical Virology, University of Zurich",
"SEQUENCING.Sequencing_lab_name": null,
"SEQUENCING.Library_preparation_kit": null,
"SEQUENCING.Sequencing_platform": null,
"SEQUENCING.General_sequencing_purpose": "OTHER",
"SEQUENCING.Detailed_sequencing_purpose": false,
"RAW_DATASET.Raw_data_coverage": null,
"RAW_DATASET.Raw_data_embargo_date": null,
"RAW_DATASET.Raw_data": false,
"ASSEMBLY.Assembly_method": null,
"ASSEMBLY.Assembly_length": 29862,
"ANNOTATION_PANGOLIN.Pangolin_lineage": "B.1.1",
"ANNOTATION_PANGOLIN.Pangolin_scorpio_lineage": "",
"ANNOTATION_PANGOLIN.Pangolin_version": "4.3.1",
"ANNOTATION_NEXTCLADE.Nextclade_clade": "20B",
"ANNOTATION_NEXTCLADE.Nextclade_pangolin_lineage": "B.1.1",
"ANNOTATION_NEXTCLADE.Substitutions": "C241T,C3037T,C14408T,A23403G,G28881A,G28882A,G28883C,T29148C",
"ANNOTATION_NEXTCLADE.Deletions": "",
"ANNOTATION_NEXTCLADE.Insertions": "",
"ANNOTATION_NEXTCLADE.Amino_acid_substitutions": "N:R203K,N:G204R,N:I292T,ORF1b:P314L,S:D614G",
"ANNOTATION_NEXTCLADE.Amino_acid_deletions": "",
"ANNOTATION_NEXTCLADE.Amino_acid_insertions": "",
"ANNOTATION_NEXTCLADE.Frameshifts": "",
"ANNOTATION_NEXTCLADE.Missing": "",
"ANNOTATION_NEXTCLADE.Total_missing": 0,
"ANNOTATION_NEXTCLADE.Non_ACGTNs": "",
"ANNOTATION_NEXTCLADE.Total_non_ACGTNs": 0,
"ANNOTATION_NEXTCLADE.Private_mutations_-_Labeled_substitutions": "",
"ANNOTATION_NEXTCLADE.Private_mutations_-_Reversions": "",
"ANNOTATION_NEXTCLADE.Private_mutations_-_Unlabeled_substitutions": "T29148C",
"ANNOTATION_NEXTCLADE.Private_mutations_-_Total_labeled": 0,
"ANNOTATION_NEXTCLADE.Private_mutations_-_Total_reversions": 0,
"ANNOTATION_NEXTCLADE.Private_mutations_-_Total_unlabeled": 1,
"ANNOTATION_NEXTCLADE.Private_mutations_-_Total_private": 1,
"ANNOTATION_NEXTCLADE.Private_mutations_-_QC_total": 1,
"ANNOTATION_NEXTCLADE.Private_mutations_-_QC_status": "good",
"ANNOTATION_NEXTCLADE.Total_PCR_primer_changes": 0,
"ANNOTATION_NEXTCLADE.Nextclade_QC_score": 0,
"ANNOTATION_NEXTCLADE.Nextclade_QC_status": "good",
"ANNOTATION_NEXTCLADE.Nextclade_version": "3.8.2",
"EXTERNAL_IDENTIFIER.GISAID_identifier": "EPI_ISL_524474",
"EXTERNAL_IDENTIFIER.ENA_sample_identifier": "ERS6146590",
"EXTERNAL_IDENTIFIER.ENA_project_identifier": "PRJEB43828",
"EXTERNAL_IDENTIFIER.ENA_analysis_identifier": "ERZ1765023",
"EXTERNAL_IDENTIFIER.ENA_sequence_id_identifier": "FR990296.1",
"EXTERNAL_IDENTIFIER.ENA_experiment_identifier": null,
"EXTERNAL_IDENTIFIER.ENA_run_identifier": null,
"FRAMESHIFTS.Frameshift_position": false,
"FRAMESHIFTS.Frameshift_diagnosis": false
}
]
}
GET /{dataset}/{category}/submissions
Description
Get the list of all submissions of a given category in a dataset by week.
Try it out
https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/submissions
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/submissions" -H "accept: application/json"
Example response
[
{
"submissions_nb": 3154,
"week": "2021-03-29"
},
{
...
},
{
"submissions_nb": 46,
"week": "2024-08-26"
}
]
GET /{dataset}/{category}/stats
Description
Get the statistics of a given category of a dataset.
Try it out
https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/stats
cURL
curl -X GET "https://spsp.sib.swiss/api/v1/viruses/sars-cov-2/stats" -H "accept: application/json"
Example response
{
"species": "all",
"sample_nb": 164600,
"raw_datasets_nb": 141449,
"assemblies_nb": 164600,
"last_submission_date": "2024-08-29"
}
Contact
For any question or suggestion on SPSP, please send an email to SPSP support.