API for COSMIC Mutation Data
This API provides information from the COSMIC mutation data set provided by the Sanger Institute, which includes both GRCh37 and GRCh38.
Due to the source data's terms of use, this API does not support pagination.
Source files (requires a login account to access) are available from the COSMIC download page.
This service is provided "as is" and free of charge. Please see the Frequently Asked Questions page for more details on terms of service, etc.API Demo
The following demo shows how this API might be used with an autocompleter we've developed. (Example: Try typing SP.)
For further experimentation with the autocompleter and this API, try the autocompleter demo page.
API Documentation
API Base URL: https://clinicaltables.nlm.nih.gov/api/cosmic/v4/search (+ query string parameters)
This data set may also be accessed through the FHIR ValueSet $expand operation.
In addition to the base URL, you will need to specify other parameters. See the query string parameters section below for details.
Query String Parameters and Default Values
At a minimum, when using the above base URL, you will need to specify the "terms" parameter containing a word or partial word to match.
Parameter Name | Default Value | Description |
---|---|---|
terms | (Required.) The search string (e.g., just a part of a word) for which to find matches in the list. More than one partial word can be present in "terms", in which case there is an implicit AND between them. | |
maxList | Optional, with a default of 7. Specifies the number of results requested, up to the upper limit of 500. If present but the value is empty, 500 will be used. | |
q | An optional, additional query string used to further constrain the results returned by the "terms" field. Unlike the terms field, "q" is not automatically wildcarded, but can include wildcards and can specify field names. See the Elasticsearch query string page for documentation of supported syntax. | |
grchv | 37 | Genome Reference Consortium Human build version, either 37 or 38. |
df | MutationID, GeneName, MutationCDS, MutationAA | A comma-separated list of display
fields (from the fields section below) which are
intended for the user to see when looking at the results. The parameter "ef" (see below) may also be used to specify the data fields to retrieve. The main difference is that the value of "df" is always a string (for display), while the value for "ef" could be a json object when the field value has a complex structure. |
sf | All fields | A comma-separated list of fields to be searched. |
cf | MutationID | A field to regard as the "code" for the returned item data. |
ef | A comma-separated list of additional fields to be
returned for each retrieved list item. (See the Output format section for how the data for fields
is returned.) If you wish the keys in the returned data hash to be something
other than the field names, you can specify an alias for the field name by
separating it from its field name with a colon, e.g.,
"ef=field_name1:alias1,field2,field_name3:alias3,etc. Note that not
every field specified in the ef parameter needs to have an alias. The parameter "df" (see above) may also be used to specify the data fields to retrieve. The main difference is that the value of "df" is always a string (for display), while the value for "ef" could be a json object when the field value has a complex structure. |
COSMIC Field Descriptions
Field | Field Description (Description text taken from the COSMIC website.) |
---|---|
AccessionNumber | The transcript identifier of the gene. |
GeneCDS_Length | Length of the gene (base pair) counts. This field has empty value for all records. It is no longer available in the COSMIC data download and the field is preserved for backward compatibility |
GeneName | The gene name for which the data has been curated in COSMIC. In most cases this is the accepted HGNC identifier. |
HGNC_ID | If gene is in HGNC, this id helps linking it to HGNC. |
MutationAA | The change that has occurred in the peptide sequence. |
MutationCDS | The change that has occurred in the nucleotide sequence. |
MutationDescription | Type of mutation (substitution, deletion, insertion, complex, fusion, unknown etc.) |
MutationGenomePosition | The genomic cooridnates of the mutation. |
MutationStrand | Positive or negative. |
MutationID | Unique mutation identifier, also called alternative mutation identifier in COSMIC. |
LegacyMutationID | Legacy mutation identifier. It was called MutationID in v89 and earlier. |
GenomicMutationID | Genomic mutation identifier, |
Name | A field constructed by concatenating AccessionNumber, GeneName, MutationCDS and MutationID. |
PrimaryHistology | The histological classification of the sample. |
PrimarySite | The primary tissue/cancer from which the sample originated |
PubmedPMID | The PUBMED ID for the paper that the sample was noted in, linking to pubmed to provide more details of the publication. |
Site | PrimarySite and PrimaryHistology. |
GRChVer | The Genome Reference Consortium Human build version, can be either 37 or 38. |
COSMIC_GENE_ID | The unique COSMIC gene identifier (COSG). |
COSMIC_PHENOTYPE_ID | The unique COSMIC identifier (COSO) for the classification. |
Output format
Output for an API query is an array of the following elements:
- The total number of results on the server, which can be more than the number of results returned. This reported total number of results may also be significantly less than the actual number of results and is limited to 10,000, which may significantly improve the service response time.
- An array of codes for the returned items. (This is the field specified with the cf query parameter above.)
- A hash of the "extra" data requested via the "ef" query parameter above. The keys on the hash are the fields (or their requested aliases) named in the "ef" parameter, and the value for a field is an array of that field's values in the same order as the returned codes.
- An array, with one element for each returned code, where each element is an array of the display strings specified with the "df" query parameter.
- An array, with one element for each returned code, where each element is the "code system" for the returned code. Note that only code-system aware APIs will return this array.
Sample API Queries
Query | Result | Description |
---|---|---|
https://clinicaltables.nlm.nih.gov/api/cosmic/v4/search?terms=aff2 | [24995,["35664913","35685107","35691722","35673444","35670952","35656831","35680716"],null,[["35664913","AFF2","c.*7015del","p.?"],["35685107","AFF2","c.*4165dup","p.?"],["35691722","AFF2","c.*7432dup","p.?"],["35673444","AFF2","c.*8067del","p.?"],["35670952","AFF2","c.*143dup","p.?"],["35656831","AFF2","c.*8057dup","p.?"],["35680716","AFF2","c.*8979C>A","p.?"]]] | Finds gene names containing "AFF2" from the COSMIC data set. Seven of 24995 Mutation IDs are returned as code fields, no extra data was requested ("ef" was not specified in the URL), and finally the four (default) display fields for each record are returned. |