Lurbinah Week 10

From OpenWetWare
Jump to navigationJump to search

Lizzy Urbina

Template:lurbinah

Assignments


Weekly Assigments

Class Journal Assigments

Purpose

The purpose of this week's assignment was to critically analyze LncTarD database and determine if it is an overall good database in terms of quality of scientific work, effectiveness, and how friendly it is to use.

Choosing a Database

  • Databases to select were found in Nucleic Acids Research Database Issue Table of Contents 2020
  • LncTarD was chosen to be analyzed.
    • Hongying Zhao, Jian Shi, Yunpeng Zhang, Aimin Xie, Lei Yu, Caiyu Zhang, Junjie Lei, Haotian Xu, Zhijun Leng, Tengyue Li, Waidong Huang, Shihua Lin, Li Wang, Yun Xiao, Xia Li, LncTarD: a manually-curated database of experimentally-supported functional lncRNA–target regulations in human diseases, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D118–D126, https://doi.org/10.1093/nar/gkz985

Database Evaluation

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?
  3. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
  4. What type of data source does it have?
    1. primary versus secondary ("meta")?
    1. curated versus non-curated?
      1. if curated, is it electronic versus human curation?
      2. if human curation, is it in-house staff versus community curation?
  5. What individual or organization maintains the database?
    1. public versus private
    2. large national or multinational entity or small lab group
    3. University, (http://bio-bigdata.hrbmu.edu.cn/LncTarD/index.jsp)
  6. What is their funding source(s)?

Scientific quality of the database

  1. Does the content appear to completely cover its content domain?
    1. How many records does the database contain?
      • From their home page "LncTarD includes 2822 experimentally-supported functional regulations and expression associations in 177 human diseases, including 475 lncRNAs, 391 miRNAs, 774 protein-coding genes and 140 biological functions." (http://bio-bigdata.hrbmu.edu.cn/LncTarD/)
    2. What claims do the database owners make about coverage in the corresponding paper?
      • From the article "The current version of LncTarD includes 2822 disease-associated lncRNA–target regulations, including 1613 experimentally-supported functional regulations and 1209 expression associations, involving 475 lncRNAs and 1039 targets contributing to 140 biological functions in 177 human diseases. " (https://academic.oup.com/nar/article/48/D1/D118/5622712#190995964)
  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?
    1. yes it is. From Article "LncTarD, a novel database that collects and integrates disease-associated lncRNA–target regulations into a comprehensive resource for the first time" (https://academic.oup.com/nar/article/48/D1/D118/5622712#190995964)
  4. Is the database content timely?
  5. Is there a need in the scientific community for such a database at this time?
    • Yes, it is needed for advances in cancer therapy. From the article "Understanding the precise molecular mechanisms by which lncRNA regulates downstream key mediators to affect important biological functions is necessary to help explain the roles of lncRNAs in the pathogenesis of human diseases and will be a critical first step in exploring these potential new avenues in cancer therapy." (https://academic.oup.com/nar/article/48/D1/D118/5622712#190995964)
  6. Is the content covered by other databases already?
  7. How current is the database?
    • I could not find this information in the article, page, or search engine.
    1. When did the database first go online?
      • I could not find this information in the article, page, or search engine.
    2. How often is the database updated?
      • It depends on submission and peer review to be published. see question number four.
    3. When was the last update?

General utility of the database to the scientific community

  1. Are there links to other databases? Which ones?
  2. Is it convenient to browse the data?
  3. Is it convenient to download the data?
    1. In what file formats are the data provided?
      • See question above
    2. What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
      • See question above
    3. Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
      • See questions above
  4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
    1. Is the website well-organized?
    2. Does it have a help section or tutorial?
    3. Are the search options sensible?
    4. Run a sample query. Do the results make sense?
  5. Access: Is there a license agreement or any restrictions on access to the database?
    • The user can run different runs and dowload the program but all right are reserved by the College of Bioinformatics Science and Technology, Harbin Medical University. (http://bio-bigdata.hrbmu.edu.cn/LncTarD/)

Summary judgment

  1. Would you direct a colleague unfamiliar with the field to use it?
    • I think this website is very specif and the person would need a lot of background information in order to use it to its fullest potential.
  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.
    • It is definitely a professional database, it contains a lot of information, and its a breaking ground database.

Conclusion

LncTard is a new database with a lot of breaking groud information that allows scientists in the field to have a better understanding of LncRNA, and its possible use in therapies to fight cancer. I consider it a very professional database to be used by people with some knowledge about the topic, it is well organized and easy to use.

Acknowledgments

  • I copied and modified the protocol from Week 10 for this assignment.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Lurbinah (talk) 22:34, 11 May 2020 (PDT)

References

  • OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved May 11, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10
  • Hongying Zhao, Jian Shi, Yunpeng Zhang, Aimin Xie, Lei Yu, Caiyu Zhang, Junjie Lei, Haotian Xu, Zhijun Leng, Tengyue Li, Waidong Huang, Shihua Lin, Li Wang, Yun Xiao, Xia Li, LncTarD: a manually-curated database of experimentally-supported functional lncRNA–target regulations in human diseases, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D118–D126, https://doi.org/10.1093/nar/gkz985 Retrieved May 11,2020
  • Daniel J Rigden, Xosé M Fernández, The 27th annual Nucleic Acids Research database issue and molecular biology database collection, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D1–D8, https://doi.org/10.1093/nar/gkz1161 Retrived May 11, 2020
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Lurbinah_Week_10&oldid=1084325"