ProteomicsDB: toward a FAIR open-source resource for life-science research.
Ludwig Lautenbacher1, Patroklos Samaras2, Julian Muller2
1Technical University of Munich, Computational Mass Spectrometry, 85354 Freising, Bavaria, Germany.
Nucleic Acids Research
|November 18, 2021
Summary
ProteomicsDB enhances data accessibility with a new API and open-source UI, improving FAIR data principles and integrating AI for peptide analysis. This update expands its multi-omics and multi-organism research capabilities.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- ProteomicsDB is a vital resource for multi-omics and multi-organism life science research.
- Previous versions focused on data aggregation and accessibility.
Purpose of the Study:
- To enhance the findability, accessibility, interoperability, and reusability (FAIR) of ProteomicsDB data.
- To introduce new features and integrations for improved data analysis and visualization.
- To expand the resource's data content and organism coverage.
Main Methods:
- Development and release of a new application programming interface (API) for systematic data access.
- Introduction of a new open-source user interface (UI) with enhanced visualization tools.
- Integration of the deep-neural-network Prosit for peptide fragmentation and retention time prediction.
- Expansion of data content to include new human biology experiments and a novel organism.
Main Results:
- Improved data accessibility and interoperability through the new API and UI.
- Enhanced data visualization capabilities, including protein structure and spectrum viewing.
- Establishment of an automatic processing pipeline for reevaluating database search engine results.
- Increased data diversity with new experimental data and organism support.
Conclusions:
- The updated ProteomicsDB significantly advances FAIR data principles in proteomics research.
- New features and integrations empower the scientific community with advanced analytical tools.
- ProteomicsDB continues to be a comprehensive and evolving resource for life science research.
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