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Updated: Oct 28, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Refget: standardized access to reference sequences.

Andrew D Yates^1,2, Jeremy Adams^2,3, Somesh Chaturvedi^1,4

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Bioinformatics (Oxford, England)

|July 14, 2021

Summary

This summary is machine-generated.

We developed refget, a new API standard for accessing genomic reference sequences. This ensures consistent data retrieval for bioinformatics, improving genomic sequencing workflows.

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Last Updated: Oct 28, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Published on: January 25, 2019

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Bioinformatics
Genomics
Data Standards

Background:

Reference sequences are foundational for bioinformatics, particularly in genomic sequencing.
Standardized access to these sequences is crucial for reproducible research and common bioinformatics methods.

Purpose of the Study:

To establish a standardized API specification for accessing reference sequences and sub-sequences.
To provide a robust framework for consistent data retrieval in genomics.

Main Methods:

Developed the refget API specification under the Global Alliance for Genomics and Health framework.
Created four reference implementations across diverse infrastructures (in-house and cloud).
Established a compliance suite and web report for verifying implementation conformity.

Main Results:

The refget specification provides a novel method for accessing reference sequences via sequence-derived identifiers.
Four compliant reference implementations demonstrate the specification's versatility and feasibility.
The compliance suite ensures interoperability and adherence to the standard.

Conclusions:

The refget specification offers a standardized and efficient way to access genomic reference data.
This standard facilitates reproducible bioinformatics analyses and advances genomic data sharing.