@labinfo/hgnc-get-gene-info v1.0.3

HGNC Gene Info Wrapper

This package is designed to facilitate interactions with the Human Gene Nomenclature Committee (HGNC) API. It enables the retrieval of genetic information using specific methods based on stored or searchable fields

Properties

• rootURL: string: Base URL for API requests to HGNC. Default value is 'https://rest.genenames.org'.
• frontRootURL: string: Base URL for requests to HGNC Site. Default value is 'https://www.genenames.org'.
• output: "XML" | "JSON": Desired output format for the API responses. Possible values are 'XML' or 'JSON', with 'JSON' being the default.

Methods

• fetchInfo(): Returns general information available from the API.
• fetchBy(storedField: string, query: any): Fetches information from the API based on a specific field and a query. Throws an error if the specified field is not in the storedFields list.
• searchByAllFields(query: any): Conducts a search on all searchable fields with the specified query.
• searchBy(searchableField: string, query: any): Conducts a search on a specific field with the specified query. Throws an error if the specified field is not in the searchableFields list.
• dbOverview(dumentType:string): Returns general information from database.

Accessible Properties

• storedFields: Returns a list of fields that can be specified for the fetchBy method.
• searchableFields: Returns a list of fields that can be specified for the searchBy method.
• documentTypes: Return s list of fields that can br specified for th dbOverview method.

Usage Examples

Creating an Instance of the Class

const hgnc = new HGNC();

Fetching General Information

The information request (https://rest.genenames.org/info) is utilized to obtain details about the service itself rather than to retrieve data from the server. The response from this request will provide information such as the last update time of the server data (lastModified), the total number of documents (numDoc), which fields are searchable through search and fetch methods (searchableFields), and which fields can be returned by the fetch operation (storedFields).

async () => {
  const info = await hgnc.fetchInfo();
};

Fetching by a Specific Field

The fetch request is the primary method used to obtain specific records from the server, which will include all fields listed in the "storedFields" section of the info response. The fetch operation requires the user to specify a queryable field (as detailed in the "searchableFields" section of the info) along with the search term in the URL.

The definition list below shows all the fields that could possibly be returned within a fetch request:

async () => {
  const resource = "ensembl_gene_id";
  const query = "ENSG00000166526";
  const data = await hgnc.fetchBy(resource, query);
};

Search

The search request is more powerful than the fetch for querying the database, but the search only returns the fields hgnc_id, symbol, and score. If you want to retrieve all the data for a set of genes from the search results, the user could use the hgnc_id returned by the search to then initiate a request for the hgnc_id using fetch.

Below is a definition list containing the fields that can be used to fetch and search records found within the HGNC record.

Searching by All Fields

async () => {
  const query = "BRAF";
  const data = await hgnc.searchByAllFields(query);
};

Searching by a Specific Field

Search can do more powerful request then just a simple look up on a field as seen in the examples below:

async () => {
  const resource = "symbol";
  const query = "ZNF*"; // Return all records that have symbols that start with ZNF
  const data = await hgnc.searchBy(resource, query);
};

async () => {
  const resource = "symbol";
  const query = ":ZNF*+NOT+status:Approved"; // Return all records that have symbols that start with ZNF which are not approved
  const data = await hgnc.searchBy(resource, query);
};

DB Overview

This method returns an overview in numbers of the database data. You can see the JSON schema of the response in this file.

async () => {
  const documentType = "gene"; // "gene", "group" or "site"
  const {response}  = await hgnc.dbOverview(documentType);
};

This document covers the basic functionalities of the HGNC class for interacting with the HGNC API, making it easier to retrieve genetic data efficiently and in a structured manner.

For more detailed documentation, access the link: HGNC REST API Help.