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PRIDE: the proteomics identifications database.

Lennart Martens1, Henning Hermjakob, Philip Jones

  • 1Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.

Proteomics
|July 26, 2005
PubMed
Summary
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High-throughput proteomics generates vast protein data. The PRIDE database makes this complex proteomics data publicly accessible and computationally queryable, improving data sharing.

Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • High-throughput proteomics technologies are rapidly increasing the number of identified proteins.
  • The publication of proteomics data, often as lengthy PDF lists, hinders computational accessibility and data reuse.
  • Existing data dissemination methods lack standardization and machine-readability.

Purpose of the Study:

  • To establish a centralized, publicly accessible database for proteomics identifications.
  • To facilitate computational access and querying of proteomics data.
  • To address the limitations of current data publication practices in proteomics.

Main Methods:

  • Development of the Proteomics Identifications (PRIDE) database.
  • Implementation of a web-based query interface.

Related Experiment Videos

  • Provision of a user-friendly data upload facility and a documented Application Programming Interface (API).

    • Main Results:

    • PRIDE provides a solution for turning publicly available proteomics data into publicly accessible data.
    • The database supports direct computational access through its API.
    • The PRIDE database, source code, and tools are freely available for web access and download.

    Conclusions:

    • PRIDE enhances the accessibility and usability of proteomics data.
    • The database promotes data sharing and reuse within the scientific community.
    • Standardized data submission and access are crucial for advancing proteomics research.