ColinWikholm BIOL368 Week 14

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Purpose

To explore and learn to use biological databases freely accessible online, and to focus on and share information about an individually selected biological database.

Methods and Results

Part 1: Biological Databases

Assignment: Database Profile

  1. Choose a database for investigation. Which did you choose?
  2. Describe the database's purpose.
    • To provide a collection of genome, cell, organism, and ecology databases that allows for micro-macro integration of information for the sake of biology research, as well as applications in human health.[1]
  3. What biological information does it cover?
    • The KEGG Database provides a wide-range of biological information, including genomic, chemical, systems, and health data. The systems information includes pathway maps, biological hierarchies, and modules that allow for genomic sequence identification and interpretation. The genomic information includes orthologs, entire genomes, genes and polypeptides, and genetic sequence similarities. The chemical information includes small molecules, glycans, chemical reactions in biological systems, classes of reactions, and enzymes. Finally, the health information includes human diseases, drugs and their groups, and substances relevant to human health.[2]
  4. What species are included?
    • The KEGG Database does not have a specified selection of acceptable organisms, and has complete genomes of 346 Eukaryotes, 3944 Bacteria, and 237 Archaea. However, it contains considerable health data that is focused around human (Homo sapien) biochemistry, drugs, and health.[3]
  5. What questions can it be used to address in biology?
    • There are countless questions that could be answered using KEGG. For example, how do these two drugs interact chemically, and how could this affect my health? Also, what is the genomic sequence of this bacteria, and how does this relate to cellular functioning and ecosystem interactions? Finally, what are the known metabolic pathways of the human body?[4]
  6. What kind of database is it? Who maintains it?
    • KEGG, like its name Kyoto Encyclopedia of Genes and Genomes implies, is a collection of biological data of all levels (from chemical to organismal to ecosystems). It is a "meta" database that is developed and maintained electronically by Kanehisa Laboratories. The GenomeNet website that mirrors the KEGG Database is maintained electronically by the Kyoto University Bioinformatics Center.[5]
  7. Who/What is their source of funding?
    • Previously government-funded, the KEGG Database now receives substantial community funding. The KEGG MEDICUS is funded by Japan's National Bioscience Database Center (NBDC), and the rest is primarily funded by academic subscriptions and commercial licencing.[6]
  8. Are there licence stipulations or restriction to access?
    • The KEGG Database is free to access online, but the "KEGG FTP site for academic users" is only accessible by paid subscribers. Commercial use of KEGG by companies requires a licence from Pathway Solutions Inc.
  9. How often is the database updated, and when was it's most recent update?[7]
    • The database is updated about once a month, with its most recent update on November 1, 2016.[8]
  10. Does it provide links to other databases?
    • Yes, KEGG gives links to numerous other databases including PubMed, MeSH, EXPaSy, SCOP, and many others.[9]
  11. Can information be downloaded, and if so, in what types of files?
    • Yes, files can be downloaded in two format types: flat-file format and the relational database format.[10]
  12. How user friendly is the database?
    • Is it organized well?
      • Kegg is very well-organized and uses ordinary language. It utilizes many easy to understand figures, tables, and diagrams that are accessible to ordinary people.[11]
    • Is there a help section/tutorial
      • Kegg does not have a section labeled as a "help" or "tutorial" sections, but easy to understand instructions and descriptions are given for how to search the database and use its various tools.[12]
    • Perform a sample query and evaluate if the results make sense
      • I searched the KEGG database for "HIV-1" and it returned data for HIV-1 enzymes, metabolic interactions, the HIV-1 Viral Protein R, and other related information. The results make sense, and give data related to detailed or large-scale HIV-1 interactions.[13]

Part 2: Group Journal Club

All work and finished project can be found at Matt Oki's Individual Journal Week 14

Acknowledgments

I would like to thank Dr. Kam Dahlquist for her sharing of information in-class on November 22 regarding file formatting and data storage within databases. For the Week 14 slides and journal club assignment, I worked with Matt Oki, Matt A., and Mia Huddleston in class on November 28, 2016, as well as daily over Facebook messenger until completion of the assignment on December 5, 2016. We worked together over Google Slides and on Matt Oki's Individual Journal Page Week 14. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Colin Wikholm 19:04, 22 November 2016 (EST)


Signature for group project:

Colin Wikholm 02:35, 6 December 2016 (EST)

References

  1. Hebly, Marit, et al. "Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles." Applied and environmental microbiology 80.14 (2014): 4433-4449. doi:10.1128/AEM.00785-14
  2. Kegg Database
  3. Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659. DOI: 10.1038/31405
  4. Müller, F. (2009). Assessing Antibody Neutralization of HIV-1 as an Initial Step in the Search for gp160-based Immunogens (Doctoral dissertation, Universität des Saarlandes Saarbrücken).
  5. Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6.
  6. Tran, E. E., Borgnia, M. J., Kuybeda, O., Schauder, D. M., Bartesaghi, A., Frank, G. A., ... & Subramaniam, S. (2012). Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog, 8(7), e1002797. http://dx.doi.org/10.1371/journal.ppat.1002797
  7. Wilen CB, Tilton JC, Doms RW. HIV: Cell Binding and Entry. Cold Spring Harbor Perspectives in Medicine. 2012;2(8):a006866. doi:10.1101/cshperspect.a006866.

Important links

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

User:Colin Wikholm

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