Jmenzago Week 9

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Purpose

Assignment

General information about the database

  1. What is the name of the database? (link to the home page)
  2. What type (or types) of database is it?
    1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
    2. What type of data source does it have?
      • primary versus secondary ("meta")?
      • curated versus non-curated?
        • if curated, is it electronic versus human curation?
          • if human curation, is it in-house staff versus community curation?
  3. What individual or organization maintains the database?
    • Lab groups from the College of Pharmaceutical Sciences, Zhejiang University
      • Lab of Innovative Drug Research and Bioinformatics
      • Lab of Drug Metabolism and Pharmaceutical Analysis
  4. What is their funding source(s)?

Scientific quality of the database

  1. Does the content appear to completely cover its content domain?
    • How many records does the database contain?
      • Provides info about 266 drug transporters
        • Transport 585 FDA approved drugs and 246 Clinical/Preclinical drugs for 414 diseases
    • What claims do the database owners make about coverage in the corresponding paper?
  2. What species are covered in the database? (If it is a very long list, summarize.)
  3. Is the database content useful? I.e., what biological questions can it be used to answer?
  4. Is the database content timely?
    • Is there a need in the scientific community for such a database at this time?
    • Is the content covered by other databases already?
  5. How current is the database?
    • When did the database first go online?
    • How often is the database updated?
    • Last updated June 1, 2019

General utility of the database to the scientific community

  1. Are there links to other databases? Which ones?
    • No
  2. Is it convenient to browse the data?
  3. Is it convenient to download the data?
    • In what file formats are the data provided?
      • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
      • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
  4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
    • Is the website well-organized?
    • Does it have a help section or tutorial?
    • Are the search options sensible?
    • Run a sample query. Do the results make sense?
  5. Access: Is there a license agreement or any restrictions on access to the database?

Summary judgment

  1. Would you direct a colleague unfamiliar with the field to use it?
  2. Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, and seems amateur.

Scientific Conclusion

Acknowledgments

References

  • J. Y. Yin, W. Sun, F. C. Li, J. J. Hong, X. X. Li, Y. Zhou, Y. J. Lu, M. Z. Liu, X. Zhang, N. Chen, X. P. Jin, J. Xue, S. Zeng*, L. S. Yu* & F. Zhu*. VARIDT 1.0: Variability of Drug Transporter Database. Nucleic Acids Research. 48(D1): D1042-D1050 (2020). PMID: 31495872
  • OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved March 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10

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