A very interesting article by Gary Bader, entitled Open Access and Open Source Speed Computational Network Biology Research, was posted on 9 April 2007 at the University of Toronto’s Project Open Source|Open Access website. Excerpts:
A major challenge for studying the cellular network is collecting all known public information from very diverse sources, such as the biomedical literature, raw experimental data and the hundreds of existing pathway databases. Open access content and open source software systems are critical for overcoming this challenge. Once information is freely shared in open, standard formats, it can be aggregated, integrated, searched, visualized and analyzed.
Pathway Commons will be a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.
As one example of why such a database might be accessed, consider the OA article e-published on 22 March 2007 by Bowie MB, Kent DG, Dykstra B, McKnight KD, McCaffrey L, Hoodless PA, Eaves CJ, Identification of a new intrinsically timed developmental checkpoint that reprograms key hematopoietic stem cell properties, Proc Natl Acad Sci USA. 2007(Apr 3);104(14):5878-82. An excerpt:
Preliminary analysis of the molecular mechanism(s) involved (18) indicates that it affects a pathway affected by c-kit, a key receptor in mouse HSC self-renewal control and one whose activation differentially regulates fetal and adult HSC self-renewal both in vivo and in vitro (12, 28).
Entry of c-kit into the Search Pathway Commons box at the Pathway Commons site yields Pathway: Signaling events mediated by Stem cell factor receptor (c-Kit).
Pathguide currently contains information about 224 biological pathway resources. Many are freely available.
These examples illustrate the urgent need for agencies that support research to put into place policies of the kind being developed by the Canadian Institutes of Health Research (CIHR), on Access to Research Outputs.