Jmenzago Week 9

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Purpose

The purpose of this assignment is to evaluate a biological database published in the 2020 Nucleic Acids Research Database issue by practicing information literacy to determine the quality of the selected database.

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?])
      • When looking at query results for DTs:
        • DT ID, Gene name, protein name, synonyms, DT family, and tissue specificity
        • Function, diseases it is related to, a list of drugs it transports (approved, clinical, preclinical, or withdrawn), and endogenous factors
        • links to pages on the database that give info about epigenetic regulations, genetic polymorphisms, disease specific protein abundances, species/tissue specific protein abundances, and exogenous factors
      • When looking at query results for drugs:
        • Drug ID, drug name, synonyms, drug type, therapeutic class
        • Chemical information (structure, formula, etc.)
        • A list of what DTs transport this drug
    2. What type of data source does it have?
      • secondary
      • curated
        • unknown what type of 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)?
    • National Key R&D Program of China
    • National Natural Science Foundation of China
    • Fundamental Research Fund for Central University
    • Innovation Project on Industrial Generic Key Technologies of Chongqing
    • Leading Talent of “Ten Thousand Plan”- National High-Level Talents Special Support Plan

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 (DTs)
        • 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?
      • To briefly summarize, they claim that there is no database that provides information about DTs to the depth and scale that they do
  2. What species are covered in the database? (If it is a very long list, summarize.)
    • The database provides information about drugs and drug transporters, most of which are human
      • information on the database about drugs in preclinical trials typically comes from research on mice
  3. Is the database content useful? I.e., what biological questions can it be used to answer?
    • The content in the database is important to understand for optimization of clinical and preclinical trials, and can lead to research projects that produce results important for understanding drug resistance, how to treat diseases, and disease etiology
  4. Is the database content timely?
    • Is there a need in the scientific community for such a database at this time?
      • Understanding the variability of different DTs is important for clinical and preclinical trials, which are always being performed
      • Understanding the variability of different DTs offers a base for useful research to be done on drug resistance and treatment of certain diseases, which will need to be done as long as there are diseases that do not have yet perfect cures
    • Is the content covered by other databases already?
      • there are other databases that provide information about DTs, however:
        • some databases contain info about DTs as a part of a collection of other data (i.e. UniProt)
        • some databases include general classification and categorization of human transporters (i.e. TCDB)
        • some databases include the association between disease and the genetic polymorphism of transporters (i.e. ABCA4Database)
        • some databases include exogenous chemicals modulating the activity of ∼50 DTs (i.e. UCSF-FDA)
      • According to the creators of the database, no other database provides this much information about as many DTs presented in the same way as VARIDT
        • there is little data on the epigenetic regulation of DTs
        • no other database has been constructed to simultaneously describe the multiple aspects of variability for DTs
  5. How current is the database?
    • When did the database first go online?
      • n/a
    • 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?
    • In the database itself:
      • When looking at query results for a DT:
        • NCBI
        • UniProt
        • TCDB
      • When looking at query results for a drug:
        • PubChem
        • ChEBI
        • TTD
    • Mentioned in the paper about the database:
      • PDB
      • KEGG
      • ChEMBL
      • DrugBank
      • TransportDB
      • HMPAS
      • METscout
      • ABCA4Database
      • SCN1A Variant Database
      • PharmGKB
      • IUPHAR-DB
      • OMIM.org
      • SLC TABLES
      • UCSF-FDA
      • Transformer
      • Metrabase
  2. Is it convenient to browse the data?
    • Yes
  3. Is it convenient to download the data?
    • Yes
    • In what file formats are the data provided?
      • All data is downloaded as text (.txt)
      • All data is in the standard format
  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?
      • Yes
    • Does it have a help section or tutorial?
      • Yes
    • Are the search options sensible?
      • Yes
    • Run a sample query. Do the results make sense?
      • Yes
  5. Access: Is there a license agreement or any restrictions on access to the database?
    • It is Open Access

Summary judgment

  1. Would you direct a colleague unfamiliar with the field to use it?
    • Yes. It is fairly easy to use, the information is well-organized, and it obtains its data from reputable databases.
  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.
    • Professional

Scientific Conclusion

The purpose of this assignment was to evaluate a database from the 2020 Nucleic Acids Research Database issue. After practicing good information literacy to evaluate the database, VARIDT was determined to be a useful and quality database. VARIDT provides useful information about the variability hundreds of drugs and drug transporters to a large scope unavailable on other databases in a user-friendly way. Their information is sourced primarily from the FDA and reputable databases like UniProt.

Acknowledgments

  • I followed the protocol on BIOL368/S20:Week 10 to complete this assignment
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jmenzago (talk) 20:46, 1 April 2020 (PDT)

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. doi: https://doi.org/10.1093/nar/gkz779
  • OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved March 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10

Assignments

Individual Journal Entries

Class Journal Entries

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