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JASPAR RESTful API: accessing JASPAR data from any programming language.
Bioinformatics. 2018 05 01; 34(9):1612-1614.B

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.

Authors+Show Affiliations

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

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29253085

Citation

Khan, Aziz, and Anthony Mathelier. "JASPAR RESTful API: Accessing JASPAR Data From Any Programming Language." Bioinformatics (Oxford, England), vol. 34, no. 9, 2018, pp. 1612-1614.
Khan A, Mathelier A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics. 2018;34(9):1612-1614.
Khan, A., & Mathelier, A. (2018). JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics (Oxford, England), 34(9), 1612-1614. https://doi.org/10.1093/bioinformatics/btx804
Khan A, Mathelier A. JASPAR RESTful API: Accessing JASPAR Data From Any Programming Language. Bioinformatics. 2018 05 1;34(9):1612-1614. PubMed PMID: 29253085.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - JASPAR RESTful API: accessing JASPAR data from any programming language. AU - Khan,Aziz, AU - Mathelier,Anthony, PY - 2017/07/07/received PY - 2017/12/14/accepted PY - 2017/12/19/pubmed PY - 2019/5/16/medline PY - 2017/12/19/entrez SP - 1612 EP - 1614 JF - Bioinformatics (Oxford, England) JO - Bioinformatics VL - 34 IS - 9 N2 - 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. SN - 1367-4811 UR - https://www.unboundmedicine.com/medline/citation/29253085/JASPAR_RESTful_API:_accessing_JASPAR_data_from_any_programming_language_ L2 - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx804 DB - PRIME DP - Unbound Medicine ER -