Dcartmel Week 10

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Purpose

The purpose of this exercise is to investigate various aspects relating to a biological database as well as it assessing its usefulness and accessibility.

Assignment

  • General information about the database
    1. What is the name of the database?
    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?
    3. What individual or organization maintains the database?
    4. What is their funding source(s)?
      • I could not find the funding source of the database. This information is not provided anywhere in their website.
  • Scientific quality of the database
    1. Does the content appear to completely cover its content domain?
      • How many records does the database contain?
      • What claims do the database owners make about coverage in the corresponding paper?
        • The database owners make claims that this database can serve as a useful source for the development of blood biomarkers that can be used to identify various types of cancer in patients. However, it is mentioned that the samples included in this database only correspond to 15 different types of cancers, and because there are a lot more cancers in existence, it can be concluded that the coverage of this domain is not complete. https://academic.oup.com/nar/article/48/D1/D789/5608990
    2. What species are covered in the database? (If it is a very long list, summarize.)
      • The species that are covered in the database are categorized as either blood data or tissue data. Each of the species corresponds to a particular type of cancer. http://bbcancer.renlab.org/download
    3. Is the database content useful? I.e., what biological questions can it be used to answer?
      • Yes, this database content is very useful. The information that it provides can aid the scientific community in the creation of biological markers that can be used to identify different types of cancer early in the diagnosis process. The biological questions that this database can be used to answer could include what the possible identifying aspects are of various types of cancer are and possibly how to create more efficient ways to diagnose particular forms of cancer.
    4. Is the database content timely?
      • Yes, I think that this database is timely because it was developed very recently in 2019. Also, such information about cancer would not lose value in terms of importance over time. http://bbcancer.renlab.org/
      • Is there a need in the scientific community for such a database at this time?
        • Yes, there is a need in the scientific community for such a database at this time because this database serves as a way for certain types of cancer to be identified while still in early stages of development, which will serve to be extremely valuable in the treatment of cancer patients.
      • 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?
        • No information available on how often the database is updated.
      • When was the last update?
  • General utility of the database to the scientific community
    1. Are there links to other databases? Which ones?
      • Yes, there are links to other databases. There are links to the GEO database, an ensembl database, the mirbase database, the pirnabank database, and the mintbase database. http://bbcancer.renlab.org/help
    2. Is it convenient to browse the data?
      • Yes, it is very convenient to browse the data in the BBCancer site because it provides downloadable links of the data. Also the data is very organized, making it easier to understand what data is being provided on the site. http://bbcancer.renlab.org/download
    3. Is it convenient to download the data?
      • Yes, it is convenient to download the data because the site provides downloadable links for its data, each being conveniently labeled. http://bbcancer.renlab.org/download
      • In what file formats are the data provided?
    4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
    5. Access: Is there a license agreement or any restrictions on access to the database?
      • No, there is no license agreement or any restrictions on access to the database. It is an open resource that anyone can utilize. http://bbcancer.renlab.org/
  • Summary judgment
    1. Would you direct a colleague unfamiliar with the field to use it?
      • No, I would not direct a colleague who is unfamiliar with this field to use it because its 'search' tab would be hard to use unless you have some kind of background in DNA/RNA analysis.
    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.
      • This database seems professional. It was created by a team of individuals that are all affiliated with universities and the information that the database contains has been included in published scientific literature.

Scientific Conclusion

The biological database that was used in this exercise seemed to be overall professionally made and contained valuable data. Since the creators of this database made the site easy to navigate and use, it can allow for the scientific community to make progress towards actually finding ways to more efficiently identify different types of cancer based on certain biological markers.

Acknowledgements

I copied and modified the Week 10 page.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Dcartmel (talk) 22:08, 1 April 2020 (PDT)

References

OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved April 1, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10.

BBCancer. (2019). Retrieved April 1, 2020, from http://bbcancer.renlab.org/.

Zuo, Z., Hu, H., Xu, Q., Luo, X., Peng, D., Zhu, K., ... & Ren, J. (2020). BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. Nucleic acids research, 48(D1), D789-D796. Retrieved April 1 2020, from https://academic.oup.com/nar/article/48/D1/D789/5608990.

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