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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
A semantic proteomics dashboard (SemPoD) for data management in translational research
Catherine P Jayapandian1, Meng Zhao, Rob M Ewing
1Division of Medical Informatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
BMC Systems Biology
|January 4, 2013
Summary
This study introduces SemPoD, a novel informatics platform that integrates 'omics data with clinical information using semantic provenance. SemPoD enables researchers to query and correlate diverse datasets, overcoming data silos in translational research.
Area of Science:
- Bioinformatics
- Translational Research Informatics
- Proteomics Data Management
Background:
- Translational research faces challenges integrating diverse 'omics data with clinical information due to data silos.
- Contextual metadata (provenance) is crucial for data integration, reproducibility, and accurate attribution but is poorly managed.
- A "provenance-aware" informatics platform is needed to address these data integration challenges.
Purpose of the Study:
- To introduce the Semantic Proteomics Dashboard (SemPoD), an ontology-driven platform leveraging semantic provenance for data integration.
- To enable researchers to query, compare, and correlate various data types across multiple projects.
- To facilitate the integration of legacy data to support ongoing translational research initiatives.
Main Methods:
- Developed SemPoD, an ontology-driven platform with a Visual Query Composer, Result Explorer, and Query Manager.
- Utilized the Systems Molecular Biology Provenance Ontology (SysPro), incorporating PROV-O, MIMIx, and MIAPE guidelines.
- Implemented a dynamic query composition interface with 'smart filtering' for efficient result set pruning.
Main Results:
- SemPoD currently supports provenance-aware querying of 1153 mass-spectrometry experiments from 20 projects.
- The SysPro ontology facilitates intuitive query composition and dynamic updates based on user selections.
- Evaluations focused on user feedback and system scalability demonstrated positive usability and functionality.
Conclusions:
- SemPoD provides an intuitive, powerful platform for accessing and querying large-scale systems biology datasets using provenance and metadata guidelines (MIAPE, MIMIx).
- The platform offers biologists an integrated view of 'omics data, enabling efficient query composition, result exploration, and query storage.
- SemPoD is deployable across various database applications and shows promise for wider adoption in 'omics' research centers.
