The BioPAX community standard for pathway data sharing

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.

PMAP: databases for analyzing proteolytic events and pathways

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis.

HLA class II molecular polymorphisms in healthy Slavic individuals from North-Western Russia

Polymerase chain reaction (PCR)-based genotyping was used to characterize the features of HLA class II molecular polymorphisms in a Slavic population of North-Western Russia. Two hundred individuals were analyzed for the DRB1 gene, and 100 persons randomly selected from this cohort were additionally typed for DQA1, DQB1 and DPB1 genes. Allele and haplotype frequencies were found to be similar to those observed in other Caucasian populations, with the exception of considerably high prevalence of the DPB1*0301 allele (16.0%) in the group studied. The high rate of diversity was observed within DRB1*04 and DRB1*14 specificities, as well as for extended DR-DQ haplotypes. In addition, significant number of "unusual" DR-DQ linkage patterns have been detected. The data seem to reflect the complexity of ethnic background of "European" Russians and may be helpful for the development of international network between donor registries.