Internet information on ion channels: Issues of access and organization

Methods in Enzymology

Volumn 294, Issue , 1999, Pages 704-731

  Conley, Edward C ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ION CHANNEL;

ARTICLE; COMPUTER SYSTEM; DATA BASE; INFORMATION SERVICE; INTERNET; PRIORITY JOURNAL;

EID: 0031760654     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(99)94040-5     Document Type: Article

References (27)

1. H. A. Lester, Science 241, 1057 (1988). See also H. O. Hsu, E. Huang, X. C. Yang, A. Karschin, C. Labarca, A. Figl, B. Ho, N. Davidson, and H. A. Lester, Biophys. J. 65, 1196 (1993), which combined heterologous coexpression of channel types and numerical simulations to analyze mechanisms of action potential generation.
2. H. A. Lester, Science 241, 1057 (1988). See also H. O. Hsu, E. Huang, X. C. Yang, A. Karschin, C. Labarca, A. Figl, B. Ho, N. Davidson, and H. A. Lester, Biophys. J. 65, 1196 (1993), which combined heterologous coexpression of channel types and numerical simulations to analyze mechanisms of action potential generation.
3. Some hyperlinks to these sites have been placed on the Ion Channel Network web site (www.le.ac.uk/csn/index.html) as an on-line companion to this article. The site supports the development of systematic nomenclatures for all ion channel gene families as an intuitive method for data organization and accession on the internet, thus illustrating the database federation strategies described herein.
4. The Biology Workbench is being developed in The Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, National Center for Supercomputing Applications (NCSA, Urbana, Illinois); see bioweb.ncsa.uiuc.edu, which includes a link to the generic Workbench interface. The specific application of the generic toolbox to ion channels under the title Ion Channel Workbench has been proposed and is under review at the time of writing.
5. Software tools for structural biology are covered in detail within other articles of this volume and are only briefly described here.
6. An aim of the GEneral NEural SImulation System (GENESIS) simulator (see also footnote 24) is to federate itself with a growing number of web databases containing neuroscientific data. Of pertinence to this article, this site discusses inherent limitations in conventional database designs including accuracy and relevance of the data entered, conflicting data, data compression, promoting participation and connection between the data and their functional significance. See also J. M. Bower, Trends Neurosci. 15, 411 (1992).
7. NEURONDB, part of Senselab (senselab.med.yale.edu/neurondb/) provides an advanced set of web-based tools to support research on neuron properties. These properties include voltage-gated conductances, neurotransmitter receptors, and neurotransmitter substances. The senselab project (funded by the Human Brain Project) has pioneered the federation of different databases (focused on the olfactory pathway) as a means to collect, analyze, and disseminate multidisciplinary neuroscience information.
8. This function is analogous to the more familiar example of flight simulators (as used for training pilots), which also compute the behavior of a complex system with high concordance to real-world measurements. Simulations optimized using evolutionary algorithm techniques (Fig. 2) can achieve ultra-high fitness in reproducing the behavior of biological systems, and should reasonably offset the skepticism which some experimentalists have for modeling approaches.
9. R. M. Eichler-West, E. De-Schutter, and G. L. Wilcox, "Using Evolutionary Algorithms to Search for Control Parameters in a Nonlinear Partial Differential Equation in Evolutionary Algorithms and High Performance Computing." Springer-Verlag, New York. 1997.
10. For example, a prototype for Caltech's database and model construction interface known as the Modeler's Workspace maintained by Jenny Forss can be accessed at http://smauggw.caltech.edu:8081.
11. M. H. Kaufman, "The Atlas of Mouse Development." Academic Press, San Diego, 1992.
12. The Gesellschaft für Biotechnologische Forschung mbH (GBF). TRANSFAC (http:// transfac.gbf.de/TRANSFAC/index.html) is being piloted for CORBA compliance at the European Bioinformatics Institute.
13. A declarative query specifies what is being searched for (see example in text) rather than a specific navigation path, e.g., 'Data/Channels/Kir/Kir2/Kir2.3.'
14. For accession outside of the Ion Channel Network/Workbench search engines, channels, and project divisions must be given distinctive names (i.e., would not tend to return false hits from random character strings when typed into a general web search engine).
15. G. A. Gutman and K. G. Chandy, Semi. Neurosci. 5, 101 (1993).
16. To date, only the alphanumeric nomenclatures of the Kv and Kir families have entered use; the principle of adopting similar alphanumeric "tags" for other ions channel families is discussed under www.le.ac.uk/csn/e00/00-38-nomenclists.html.
17. A Receptors: Classification on the Basis of Subunit Structure and Function, Pharmacol. Rev., submitted (1998).
18. There may actually be any number of entry point "synonyms" - accession numbers, ID numbers, or something similar - to represent the same biological object in a computer model, but only systematic nomenclatures can be formulated accurately without prior knowledge of the name.
19. Introduction and layout of entries, Entry 02 in E. C. Conley, and W. J. Brammar, "The Ion Channels FactsBook," Vols. I to IV. Academic Press, London, 1995, 1996, 1998, 1999.
20. The terms entered in a declarative query [square brackets in example shown] may be a numerical range, experimental conditions, or possibilities chosen from a list; named ligands, compounds, toxins, or other modulators may be specified from within an external database.
21. It should be emphasized that the random examples of objects and their elements given have no special significance in the database organization, but are merely illustrative of the kinds of information that might be included. The listings in Fig. 6 suggest many other potential objects.
22. The Ion Channel Modulators (ICM) subset of The Investigational Drugs Database (IDdb) focuses on ion channels as therapeutic drug targets and monitors drug and biotechnology patents, chemical structures, pharmaceutical actions, and clinical reports. Since the majority of drug development data is indexed either by compound name, company, or broad mechanism of action, search engines may be developed that "link-out" to specialist subscription-based sites like these (providing appropriate access privileges exist).
23. An introduction to the PubMed system (which supports the citation matching principle) is given in http://www4.ncbi.nlm.nih.gov/PubMed/.
24. In practice, citation matching approaches are far more flexible than exemplified here (e.g., using other search term types like journal name, year, title, etc.).
25. Throughout this article, the term database has been used in a limited sense of providing organized access to data; databases may actually take many different forms, e.g., a simulation program, a parameter model, an indexed list. The optimal form of data storage/retrieval will vary with the type of data.
26. See the GENESIS hypertext primer (www.bbb.caltech.edu:80/hbp/GOOD/GOOD.html), based on a chapter to appear in "Progress in Neuroinformatics" (S. Koslow and M. Huerta, eds.), Vol. 1. Lawrence Erlbaum Associates. See also J. M. Bower and D. Beeman, "The Book of GENESIS," 2nd Ed. Springer-Verlag, Berlin, 1997, which includes a CD-ROM with the GENESIS simulator TELOS.
27. See the GENESIS hypertext primer (www.bbb.caltech.edu:80/hbp/GOOD/GOOD.html), based on a chapter to appear in "Progress in Neuroinformatics" (S. Koslow and M. Huerta, eds.), Vol. 1. Lawrence Erlbaum Associates. See also J. M. Bower and D. Beeman, "The Book of GENESIS," 2nd Ed. Springer-Verlag, Berlin, 1997, which includes a CD-ROM with the GENESIS simulator TELOS.