Open AccessDevelopment of an Ocean Protein Portal for Interactive Discovery and Education
Author(s) -
Mak A. Saito,
Jaclyn K. Saunders,
Michael Chag,
David A. Gaylord,
Adam Shepherd,
Noelle A. Held,
Christopher L. Dupont,
Nicholas Symmonds,
Amber York,
Matthew Charron,
Danie Kinkade
Publication year - 2020
Publication title -
journal of proteome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.644
H-Index - 161
eISSN - 1535-3907
pISSN - 1535-3893
DOI - 10.1021/acs.jproteome.0c00382
Subject(s) - metaproteomics , data science , metadata , computer science , geospatial analysis , cyberinfrastructure , biogeochemical cycle , key (lock) , proteomics , computational biology , world wide web , biology , geography , ecology , remote sensing , biochemistry , computer security , gene
Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: "Where is my protein of interest?", "Who makes it?", and "How much is there?" and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.