RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

Sachin Gavali; Julie Cowart; Chuming Chen; Karen E Ross; Cecilia Arighi; Cathy H Wu

doi:10.1093/database/baz157

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

Database (Oxford). 2020 Jan 1:2020:baz157. doi: 10.1093/database/baz157.

Authors

Sachin Gavali¹, Julie Cowart¹, Chuming Chen^{1

2}, Karen E Ross³, Cecilia Arighi^{1

2}, Cathy H Wu^{1

3

2}

Affiliations

¹ Center for Bioinformatics and Computational Biology, 205 Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA.
² Department of Computer and Information Sciences, 101 Smith Hall, 18 Amstel Ave Newark, DE 19716, USA.
³ Department of Biochemistry and Molecular & Cellular Biology, 337 Basic Science Building, 3900 Reservoir Road, N.W, Washington D.C. 20057, USA.

Abstract

iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways.

Keywords: Cloud; Docker; Phosphoproteomics; Post-Translational Modification; RESTful API; Rust; Web Service; iPTMnet.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Computational Biology*
Data Mining
Protein Processing, Post-Translational
Proteins / genetics
Software*

Substances

Proteins

Grants and funding

U01 GM120953/GM/NIGMS NIH HHS/United States