What is the BIOBASE Knowledge Library (formerly PROTEOME) database?

What is it?

The BIOBASE Knowledge Library (BKL; formerly "PROTEOME") provides highly curated data on the proteome of selected organisms based on data extracted from the primary literature. BKL is one of the best ways to quickly assess a vast set of protein properties for a given protein, or even a set of proteins.

What is it for?

Getting a rapid understanding of a protein and all of its properties:

• Live example for the androgen receptor.
• Understanding what proteins interact with a given protein
• Determining where a protein is present or absent
• Understanding how a protein is regulated
• Comparative genomics: finding homologs, orthologs

What's in it?

• Species coverage: Homo sapiens, S. cerevisae, S. pombe, C. elegans and pathogenic fungi.
• Protein properties such as:
  • Sites of expression (presence and known absence)
  • Interacting proteins
  • Related proteins; homology; orthology
  • Regulation: Upregulated, Downregulated, Affects
  • Protein complex data
  • Protein modification data
  • Association with disease
  • Use of protein as biomarker

Unique characteristics

• Orthology: nice synteny maps are provided
• Expression patterns, including pathological and cell type, not just organ/tissue
• Highlighting of biomarker potential
• Protein modifications are listed
• Proteome's protein functions are likely to be more rigorous than those of NCBI
• Richer dataset as compared to NCBI Gene (e.g., BIOBASE has information on gene regulation, NCBI does not)
• Antibodies are listed
• Provide positive/negative correlation & data for disease and physical interactions, among others

Where to get it

As of October 2008, access to BKL no longer requires a password; only a SUNet ID is needed.

BKL improvements from PROTEOME

• Much denser reports [example]
• Vastly superior new visualizer that doesn't require a local installation [example]
• Much better navigational paradigm: left hand column provides most of the key navgiational functions.

Key references

• Proteome's list of publications
• Lane FAQ on TRANSFAC Pro, a component of BKL.
• All Lane FAQs (including access to videorecorded courses and tutorials) concerning BioBase/Proteome

Source

Lane Librarian
Record created 5/2/2006.

ypouliot, September 14, 2009