On 8th September 2023 we will be releasing the Q3 API changes for the VarSome API (stable-api.varsome.com).
The Stable API will update version 11.7.2 to version 11.8.0 with data frozen as of the 4th August 2023. This version has been successfully used in production for over a month.
The most recent version, used by VarSome itself, is always available at api.varsome.com.
The major changes introduced in version 11.8 affecting API users are listed below:
Please see the 11.8 release note for more detailed information.
The following databases have been updated:
Source |
Data Type | Current (Stable, Q2 '23) | Next Release (Stable, Q3 '23) | Comment |
AACT Clinical Trials | gene | 21-Feb-23 | 13-Jun-23 | |
ACMG classifier | variant | 11.7.2 | 11.8.0 | |
AMP classifier | variant | 11.7.2 | 11.8.0 | |
cBioPortal | variant | 21-Jun-22 | 06-Jun-23 | |
CGD | gene | 20-Oct-22 | 05-May-23 | |
ClinVar | variant | 03-Apr-23 | 31-Jul-23 | |
ClinVar | region / CNV | 03-Apr-23 | 31-Jul-23 | |
CPIC | gene | 21-Jan-23 | 06-Jun-23 | |
DGI | gene | 21-Feb-23 | 12-Jul-23 | |
Genomics England PanelAPP | gene | 22-Feb-23 | 11-Jul-23 | |
GHR | gene | 21-Feb-23 | 13-Jun-23 | |
gnomAD | variant | 3.1.2 | 3.1.2 | |
GWAS | variant | 21-Feb-23 | 11-Jul-23 | |
Jackson Laboratory CKB | gene | 22-Feb-23 | 20-Jul-23 | |
Jackson Laboratory CKB | variant | 22-Feb-23 | 20-Jul-23 | |
LUMC LOVD | variant | 04-Apr-23 | 31-Jul-23 | |
MitoMap | variant | 12-Aug-22 | 11-Jul-23 | |
NIH ClinGen | variant | 21-Feb-23 | 20-Jun-23 | |
OMIM | gene | 11-Apr-23 | 17-Jul-23 | |
OMIM | variant | 11-Apr-23 | 17-Jul-23 | |
PharmGKB | gene | 05-Mar-23 | 12-Jul-23 | |
PharmGKB | variant | 05-Mar-22 | 12-Jul-23 | |
Sanger Cosmic | variant | v97 | v98 | API customers with a valid Cosmic license |
Sanger DECIPHER | region / CNV | 21-Feb-23 | 10-Jul-23 | |
Saphetor Known Pathogenic | gene | 02-May-23 | 01-Aug-23 | All clinical classifications from all sources. |
Saphetor Known Pathogenic | variant | 02-May-23 | 01-Aug-23 | All clinical classifications from all sources. |
Pubmed | variant | 03-May-23 | 02-Aug-23 | |
UniProt Variants | variant | 20-Jan-23 | 05-May-23 |
Reminder: all the data structures returned by the VarSome API are documented here.
In GET /lookup/{spec_query}/{ref_genome} parameters, the parameters to add or exclude databases have been updated:
The response changes in this section concern both GET /lookup/{spec_query}/{ref_genome} and POST /lookup/batch/{ref_genome} requests.
The gnomad_exomes attribute in the responses has been modified to include additional information:
"nonpar": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Variant (on sex chromosome) falls outside a pseudoautosomal region"
}
The lumc_lovd attribute in the responses has been modified to include additional information:
"lovd_link": {"type": "string",
”required": false,
"read_only": false,
"label": "LOVD link"
}
Body modifications
In [POST]/lookup/genes/batch/{ref_genome} the genes array is now limited to 10.
The response changes in this section concern both GET /gene/{gene_symbol}/{ref_genome} and POST /genes/batch/{ref_genome} requests.
The responses has been modified to include additional information:
"lovd_gene": {
"type": "object",
"title": "LUMC LOVD",
"properties": {
"version": {
"type": "string",
"required": true,
"read_only": false,
"label": "LOVD Version"
},
"lovd_link": {
"type": "string",
"required": false,
"read_only": false,
"label": "LOVD link"
},
"number_of_individuals": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Number of individuals"
},
"number_of_variants": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Number of variants"
},
"phenotypes": {
"type": "array",
"title": "Phenotypes",
"items": {
"type": "object",
"properties": {
"accession": {
"type": "string",
"required": false,
"read_only": false,
"label": "Accession"
},
"source": {
"type": "string",
"required": false,
"read_only": false,
"label": "Source"
},
"term": {
"type": "string",
"required": false,
"read_only": false,
"label": "Term"
},
"inheritance_pattern": {
"type": "object",
"title": "Inheritance Pattern",
"properties": {
"accession": {
"type": "string",
"required": false,
"read_only": false,
"label": "Accession"
},
"source": {
"type": "string",
"required": false,
"read_only": false,
"label": "Source"
},
"term": {
"type": "list",
"required": false,
"read_only": false,
"label": "Term",
"items": {
"type": "string"
}
}
}
}
}
}
}
}
},
Further Information and Support
An overview of the VarSome API is available here with more detailed information here.
Please contact us at the usual address support@varsome.com should you require any additional information or run into any major issues. As ever we look forward to your feedback and suggestions to improve our platform.