FoldamerDB Review

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Purpose

The FoldamerDB database will be evaluated on categories such as professionalism, convenience, "user-friendliness", organization, and more. In addition to evaluating the quality of the database, we will also look at what types of data, sources, and species are provided in the database.

Database Evaluation

  1. First, we read the article about the database from the Nucleic Acids Research journal and then went online to the database itself.
    • For this week, both partners contributed to the same journal entry in lieu of individual journal entries.
  2. One hyperlink was provided for each of the questions in the following sections

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?
      • According to the Oxford Academic FoldamerDB article, the FoldamerDB database has entries for over 1300 peptidic foldamers collected from roughly 160 research articles. These entries present information regarding the foldamers structure, molecular properties, database ID, and more.
      1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
        • As stated on the [http://foldamerdb.ttk.hu/index.php FoldamerDB Homepage, FoldamerDB is a database that provides the experimental structure, biological activity, and identification of peptidic foldamers.
      2. What type of data source does it have?
        • FoldamerDB has secondary data sources. When viewing an individual foldamer (id: fd007), there is a citation section (in yellow) at the bottom of the page that shows any cited articles from various scientific journals. In this example, the cited article is from the journal Chemistry - A European Journal. A list of all of the cited articles can be found by clicking on the Browse Articles tab.
      3. Curated versus non-curated?
      4. If human curation, is it in-house staff versus community curation?
        • According to the Oxford Academic FoldamerDB article, the entries in the FoldamerDB database are mostly curated in-house, however, they encourage the scientific to contribute by going to the Feedback and Contribute page, which provides templates that members of the scientific community can fill out and email back to the FoldamerDB team.
    3. What individual or organization maintains the database?
      • As seen on the About Page, FoldamerDB was created in the Biomolecular Self-Assembly Group of the Research Centre for Natural Sciences. The FoldamerDB team includes a principal investigator, five data collectors, and one person in charge of concept and design.
      1. Public versus private
        • As stated on the FoldamerDB Homepage, FoldamerDB is a public database and is the first public database for peptidic foldamers.
      2. Large national, multinational entity, or small lab group?
    4. What is their funding source(s)?
      • As stated in the Funding section of the Oxford Academic FoldamerDB article FoldamerDB is funded by the Momentum Program of the Hungarian Academy of Sciences and the National Competitiveness and Excellence Program.

Scientific quality of the database

    1. Does the content appear to completely cover its content domain?
      • FoldamerDB does not completely cover its content domain. As stated in the Future Work section of the Oxford Academic FoldamerDB article, the current database focuses mainly on peptidic foldamers with mixed β-peptides. However, in the future, the FoldamerDB team, hopes to increase the number of entries in the database with the help of the scientific community.
      1. How many records does the database contain?
      2. What claims do the database owners make about coverage in the corresponding paper?
        • As stated previously, in the Oxford Academic FoldamerDB article, the database owners acknowledge that the current database mostly provides entries for mixed β-peptide peptidic foldamers, and that the scientific community needs to work on adding more entries to complete the database.
    2. What species are covered in the database? (If it is a very long list, summarize.)
      • According to the Analysis of Foldamer Types section of the Oxford Academic FoldamerDB article, the database includes 383 entries for α/β-peptide foldamers, 312 foldamers with only β-amino acids, 181 Aib foldamers, 156 foldamers with only α-amino acids, 78 peptoids foldamers, 31 γ-peptide foldamers, 20 α/γ-peptide foldamers, 22 β/γ-peptide foldamers, 23 α/β/γ-peptide foldamers, and 113 others.
    3. Is the database content useful? I.e., what biological questions can it be used to answer?
      • Yes, the database content is useful for anyone who is trying to gather information about specific foldamers. The search tab at the top of the page allows users to search for specific foldamers by entering either the FoldDB ID, Reaxys ID, or the application of the foldamer. Furthermore, the search tab can also be used to search articles by either title, author(s), journal, or year. These features make the database very useful for anyone conducting research on specific foldamers.
    4. Is the database content timely?
      • Yes, the database appears to be timely. Most of the cited articles were published within the last few years, however, some of the articles were published in the late 1990's/early 2000's.
      1. Is there a need in the scientific community for such a database at this time?
        • Yes, I think there is a need in the scientific community for such a database because, as stated in the Oxford Academic FoldamerDB article, FoldamerDB is the first public foldamer database.
      2. Is the content covered by other databases already?
    5. How current is the database?
      • As seen on the cited article page, a majority (111 out of 167) of the cited articles were published within the past 10 years, so I would consider the database pretty current.
      1. When did the database first go online?
        • The database first went online in 2019, as shown towards the bottom of the FoldamerDB Homepage.
      2. How often is the database updated?
      3. When was the last update?
        • Although FoldamerDB does not provide dates for when each entry is updated, the Browse Articles tab on the FoldamerDB website shows that the most recently published journal article used in the database was published in March of 2018.

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?
      • Yes, the user can easily navigate to sections for browsing foldamers, articles, structures, and activity. The foldamers can be browsed according to type (α Peptide, β Peptide, etc.) and source article year.
    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)?
      • There may be an error with the FoldamerDB downloading function. It is unclear how to download the data for a specific foldamer. There is, however, a download tab which navigates to a page with a single download prompt. This downloads a single standard csv file. When opened in excel this appears to contain all pertinent information for 10 foldamers, far fewer than the 1327 on the database. The text on the download page alludes to "the following links" and so we assume there are meant to be more than one.
    4. Evaluate the “user-friendliness” of the database: can a naïve user quickly navigate the website and gather useful information?
      • We would say that the website is reasonably user friendly. Each foldamer is named using their internal "FoldDB ID" nomenclature, starting with "fd0001". This is reasonable as they need some way to name these molecules. Knowledgeable users can search for foldamers with specific attributes, and naïve users won't be inundated with complex information were they to explore foldamer pages at random. Individual foldamer pages are pleasantly coloured and digestible.
    5. Is the website well-organized?
      • Yes, it is visually appealing and easily navigable.
    6. Does it have a help section or tutorial?
      • Yes, the website has a help tab with a useful "table of content[s]" that links to specific sections. This page is populated by screenshots of the website and digestible explanations.
    7. Are the search options sensible?
      • Yes, there are search, advanced search, and structure search options. Advanced search allows for searching by foldamer properties, such as molecular weight, # of H bond donors, # of H bond acceptors, Polar Surface Area, etc. Structure search allows the user to draw structures using the "JSME Molecule Editor" and search for foldamers containing the structure drawn.
    8. Run a sample query. Do the results make sense?
      • Yes, the results make sense. We used the structure search to find foldamers containing (a) benzene ring(s). This showed us a page similar to the "browse foldamers" tab. The foldamers are sorted numerically by FoldDB ID.
    9. Access: Is there a license agreement or any restrictions on access to the database?
      • No, there does not appear to be any license agreement or restrictions.

Summary judgment

    1. Would you direct a colleague unfamiliar with the field to use it?
      • We would not direct to use the FoldamerDB database unless they specifically needed information about foldamers. This is because we think that the user would lose interest quickly if they were not already familiar with foldamers or in need of information on foldamers. However, if the user did in fact need information specifically on foldamers, we think they would find this database very helpful. The advanced and structure search options would make it easy to find exactly what they need and then lead them to source articles if needed.
    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/or seems amateur.
    3. Finally, please share why you chose this database in the first place, i.e., why did it interest you? Did it live up to the expectations you had when you chose it?
      • We chose this database because of it's limited scope. We thought that this would help us in coming to definitive conclusions about the different aspects of the database. A larger database would likely require a lot more expertise to assess. This ended up being the case and we felt that we were able to assess the database fairly.

Scientific Conclusion

The FoldamerDB database generally meets our standards for professionalism, convenience, "user-friendliness", and organization. For such a small team the databased was found to be surprisingly well made and navigable, barring what is assumed to be an error on the download page. This database can serve as a useful tool for researchers in need of information on various foldamers.

Acknowledgments

  1. This FoldamerDB Review page was created jointly by Taylor Makela and Aiden Burnett
  2. We copied and modified the procedures from the Week 8 Assignment Page
  3. We explored and analyzed the FoldamerDB database for this week's assignment
  4. We also used the Oxford Academic FoldamerDB article throughout this assignment
  5. Except for what is noted above, this individual journal entry was completed by Aiden Burnett & Taylor Makela, and not copied from another source.

Taylor Makela (talk) 22:45, 28 October 2020 (PDT)

References

  1. Bilal Nizami, Dorottya Bereczki-Szakál, Nikolett Varró, Kamal el Battioui, Vignesh U Nagaraj, Imola Cs Szigyártó, István Mándity, Tamás Beke-Somfai. (2019). FoldamerDB: A Database of Peptidic Foldamers, Nucleic Acids Research. Retrieved 22 October 2020, from http://foldamerdb.ttk.hu/index.php
  2. Bilal Nizami, Dorottya Bereczki-Szakál, Nikolett Varró, Kamal el Battioui, Vignesh U Nagaraj, Imola Cs Szigyártó, István Mándity, Tamás Beke-Somfai. (2020). FoldamerDB: A Database of Peptidic Foldamers, Nucleic Acids Research. Volume 48, Pages D1122–D1128, Retrieved 22 October 2020, from https://doi.org/10.1093/nar/gkz993
  3. Dahlquist, K. (n.d.). BIOL368/F20:Week 8. Retrieved 22 October 2020, from https://openwetware.org/wiki/BIOL368/F20:Week_8

Aiden's Template

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Aiden Burnett

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Aiden Burnett Template

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Individual Journal Pages

Class Journal Pages

Taylor's Template

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