#bioinformatics #web-services #ncbi #biology #genomics #data-access #ebi

ebiotic

A Rust crate for interacting with common bioinformatics web services

7 releases

0.0.26 May 3, 2024
0.0.25 Mar 19, 2024
0.0.22 Feb 27, 2024
0.0.1 Nov 7, 2023

#50 in Biology

Download history 109/week @ 2024-02-13 162/week @ 2024-02-20 239/week @ 2024-02-27 26/week @ 2024-03-05 6/week @ 2024-03-12 247/week @ 2024-03-19 11/week @ 2024-03-26 54/week @ 2024-04-02 129/week @ 2024-04-30 2/week @ 2024-05-07

131 downloads per month

GPL-3.0 license

77KB
1.5K SLoC

Ebiotic

Crates.io Crates.io Documentation Build Status

Ebiotic provides a light-weight asynchronous interface for some popular Bioinformatics web services. It is designed to enable access to the rich data and tools provided by institutes like the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI). It's built to serialize and deserialze data using common formats like JSON and specialised bioinformatics formats like FASTA, using the Record data structure from the rust-bio library.

Disclaimer: The library does not safeguard against misuse of the endpoints (beyond hard-coded polling frequencies) and so it is important to read and understand the terms of use for each API before using this library. The library is not affiliated with any of the institutes or services it interacts with.

Installation

The library is currently in the early stages of development and is therefore not stable, but remains available on crates.io. To install, add the following to your Cargo.toml file:

[dependencies]
ebiotic = "0.0.25"

Usage

The library is designed to be simple to use and to provide a consistent interface to the various APIs. The following example demonstrates how to use the library to search the European Nucleotide Archive (ENA) for a selection of entries.

use ebiotic::data::*;

#[tokio::main]
async fn main_fasta() {
    let dbfetch = Dbfetch::default();
    let ids = DbfetchIds::new(vec!["M10051".to_string(), "M10052".to_string()]);
    let result = dbfetch.run(ids).await.unwrap().into_records();
}

The Dbfetch struct is used to create a new instance of the Dbfetch API. The DbfetchIds struct is used to create a new instance of the DbfetchIds request. The run method is then called on the Dbfetch instance with the DbfetchIds instance as an argument. The run method returns a Result which is then unwrapped and converted into a Vec<Record> using the into_records method.

In order to perform HTTP requests, a system client is required. The EbioticClient struct is used to create a new client for this purpose. By default, the EbioticClient uses an asynchronous reqwest client under the hood. This means it can be customised for platform specific requirements, such as using a proxy or customising the user agent. More information on the reqwest client can be found in the reqwest documentation.

use ebiotic::data::*;
use std::time::Duration;
use reqwest;

#[tokio::main]
async fn main_blast() {
    let client = EbioticClient::new(
        reqwest::Client::builder()
            .timeout(Duration::from_secs(10))
            .proxy(reqwest::Proxy::all("http://my-proxy:8080").unwrap())
            .build()
            .unwrap()
    );

    let dbfetch = Dbfetch::new(client, DbfetchDbs::EnaSequence, DataReturnFormats::Fasta, DbfetchStyle::Raw);
    let ids = DbfetchIds::new(vec!["M10051".to_string(), "M10052".to_string()]);
    let result = dbfetch.run(ids).await.unwrap().into_records();
}

More examples can be found in the documentation. Including how to run in synchronous code-bases using thread blocking.

Current APIs

NCBI:

  • Web-BLAST (currently only supports protein searches as it was used for another project)

EBI:

Job Dispatcher:

  • Clustal Omega

Knowledge & Data:

  • DBfetch
  • EBI Search

Contributing

Contributions are more than welcome. To implement a new endpoint follow the structure of the current modules and utilise the functionality provided by the ebiotic::core module. Alternatively, pick something from the TODO list and try to implement or find something in the code that you can improve! If you have any questions or need help, feel free to open an issue or reach out to me on via email.

TODOs

  • More tools and data sources
  • Add supplementary methods to result types (beyond just returning the data)
  • Add more tests
  • Add more documentation
  • Add more examples
  • Add more error handling
  • Add logging system beyond print statements (e.g. tracing or log crate)
  • Add more configuration options
  • Safety checks for API usage (?)
  • Citations for tools and APIs

Dependencies

~20–34MB
~548K SLoC