PADB/infoInformation about PADB


The Proteomic Analysis DataBase initiative was originally formed as a gateway for the analysis of large-scale biochemical and mass spectrometry screens of biological materials by bioinformatics and Systems Biology.
The first database to be implemented in this framework is UPdb the urinary database listing molecular species (peak maps) observed by mass spectrometry. This database will also serve as a general depository of raw mass spectrometry data from human urine samples, and researchers are encouraged to submit their data by contacting us in the first instance.

Other databases which are live:
  • LSSR (Large Scale Screening Resource), which is intended to gather existing information of expressed proteins in specific tissues from published articles. This database also contains a peptide mapping database (PepMap), which lists all peptides reportedly found by mass spectrometry screens from molecules listed in LSSR.

Other databases which are currently in the planning stages are:
  • PPID (Protein-Protein Interaction Database), a database collating reported interactions between proteins and protein/chemicals, protein clusters and pathways.
  • CluSO (Clustered sequences and Orthologs), where all protein sequences found in one species (as listed in various sequence databases) are assembled and clustered to generate a fully non-redundant and as-complete-as-possible list of proteins expressed in specific species. This database also contains the HopMap (homologue, orthologue and paralogue maps) database, which serves as an accession number unifier of molecular entries across various species.

Statistics
  • Updb total entry count: 3895
  • LSSR total entry count: 77544 (redundant) and 13359 (non-redundant)
  • PepMap total entry count: more than 500.000
  • PPID entry count: more than 8000 protein interactions (not deployed at the moment)
  • CluSO: working on the human protein set, simple datasets such as bacteria and yeast finished (not deployed at the moment)
  • HopMap: 14000 entries unified across human, rat and mouse (not deployed at the moment)

History
2014 Transfer to Glasgow
2012 PADB goes live
2010 UPdb data collection phase I and II complete
2001 PADB as a concept is born

Owner/Concepts/Main developer
Dr. Holger Husi, University of Glasgow, UK
Attribution
Prof. James Ross, University of Edinburgh, UK (LSSR, UPdb)
Prof. Kenneth Fearon, University of Edinburgh, UK (LSSR, UPdb)
Contributing members
Dr. Holger Husi, University of Glasgow, UK (data collection, curation, and deployment)
Marco Fernandes, University of Glasgow, UK (CKDdb)
Alisha Patel, University of Glasgow, UK (C/VD)
Karla Cervantes Gracia, University of Glasgow, UK (MuScle)
Scott Robinson, University of Glasgow, UK (online analysis tools)
Yoann Gloaguen, University of Glasgow, UK (multi-omics network mapping, high-level network construction)


Compile date 08-12-2016© PADB initiative