JASPAR RESTful API：从任何编程语言访问 JASPAR 数据。

JASPAR RESTful API: accessing JASPAR data from any programming language.

机构信息

Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349 Oslo, Norway.

Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0372 Oslo, Norway.

出版信息

Bioinformatics. 2018 May 1;34(9):1612-1614. doi: 10.1093/bioinformatics/btx804.

DOI:10.1093/bioinformatics/btx804

PMID:29253085

Abstract

SUMMARY

JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers.

AVAILABILITY AND IMPLEMENTATION

This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license.

CONTACT

aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

JASPAR 是一个广泛使用的开放获取数据库，其中包含经过精心整理且无冗余的转录因子结合谱。目前，可以以平面文件的形式或使用特定编程语言的接口来检索 JASPAR 中的数据。在这里，我们提出了一种与编程语言无关的应用程序编程接口 (API)，可使用代表性状态传输 (REST) 架构访问 JASPAR 数据。该 REST API 使大多数编程语言能够通过编程方式访问 JASPAR，并以八种广泛使用的格式返回数据。有多个端点可用于访问数据，还有一个端点可用于推断给定 DNA 结合域蛋白序列可能结合的 TF 结合谱。此外，它还为生物信息学工具开发人员提供了一个可交互的可浏览界面。