To support automated variant curation, you can generate queries for API calls using Mastermind API. The API calls can be used to take users to selected content in Mastermind based on modifiable input fields for disease, gene, variant and PubMed identification number (PMID).

In this post, we will detail how to make an Mastermind API call for disease, gene, variant and/or specific article.

Generating Content-Specific Mastermind API calls for Automated Variant Curation

The process of generating API calls is similar to that for generating URLs into Mastermind software. An example of a Mastermind API call is shown below.

https://mastermind.genomenon.com/api/v1/search?api_token=CUSTOM_API_TOKEN_INSERTED_HERE&disease=marfan syndrome&gene=fbn1&mutation=c1039g

API Token: The first element to note here is the”api_token=CUSTOM_API_TOKEN_INSERTED_HERE”. To secure your API token as a registered user, sign-on to the Mastermind software as you would normally, follow the link to the Mastermind API page by selecitng the Mastermind Suite drop-down in the upper right of the header bar and select API. This will take you to the Mastermind API page where you can click the link “Click here to fetch your API token“. Your custom API token will appear in the API Token field above and will replace used to insert into the “api_token=CUSTOM_API_TOKEN_INSERTED_HERE” string above.

Specifying Disease: The second element to note is the “disease=marfan syndrome” string. Diseases in Mastermind are patterned according to the Medical Subject Headings (MeSH) ontology. Commas that appear in MeSH terms remain unchanged. Information about the MeSH ontology for diseases can be found here and searches for specific entries can be performed here. Note that you may search the entire Mastermind database for articles matching your specified gene of interest by eliminating the entire “disease=marfan syndrome” string in your API call altogether.

Specifying Genes: The third element to note is the “gene=fbn1” string. Exchanging “fbn1” in this string with any other HGNC approved gene symbol will modify the URL to take you to the correct page in the Mastermind software. Information about the HGNC nomenclature can be found here.

Specifying Variants: The fourth element to note is the “mutation=C1039G” string. This permits the user to go directly to a known variant of the specified gene. Note that the variant is described at the protein level using the single letter amino acid code without any prepended “p.” as typifies HGVS nomenclature. Additional information on HGVS nomenclature can be found here. Please refer to our blog post describing in greater detail how to characterize additional variants.

Failure to input appropriately spelled or punctuated API token, disease or gene will result in an error message. An input of a variant for which Mastermind has no results will yield a “0” NULL result.

API results include the total number of articles mentioning your input parameters together as well as a direct link into the Mastermind software displaying this content to expedite variant curation efforts.