Carolyne week 10

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Purpose

The purpose of this inquiry is to evaluate the user-friendliness of the T-psi-C tRNA database to learn more about the qualities of this database and why it is important for tRNA research.

Database Information

General Information

  • 'Name: T-psi-C Database
  • Type of Database:
    • Biological Information: This database stores tRNA sequences
    • Type of Data: Primary
    • Curation: Human curation
      • The curation is done by the community, but anyone who uploads data needs to be a verified user. In addition, all uploaded data is checked by the staff to ensure that it is accurate.
  • Organization: The database is a public database. It is maintained by a group of researchers associated with the Analysis and Integration of Multiomics Data, which is a part of Institute of Human Genetics in the Polish Academy of Sciences. Additionally, one of the people who maintains the database is associated with a private company, Wozniak Technologies.
  • Funding Source: Institute of Human Genetics, Polish Academy of Sciences.

Scientific Quality of the Database

  • Content:
    • Records: The database contains 1030 tRNA sequences.
    • Coverage Claims: In the paper, they claim they have sequences from a wide vareity of sources. Of these tRNA sequences 122 are mitochonrial tRNAs, 38 are plasmid tRNAs, and 17 are viral tRNAs (Sajek et. al., 2020). The tRNA data was also obtained using different methods. 251 sequences were gained using hydro-tRNAseq, 54 sequences were found using crystal structure data, and 46 structures were gained from the Protein Data Bank (PDB) (Sajek et. al., 2020).
  • Species: This database contains information from a variety of species. Some species include the following: Homo sapiens, Aedes albopictus, Aeropyrum pernix, and Avian myeloblastosis virus. The database also tells you if the tRNA sequence is viral or if it is from the cytoplasm, mitochondria, or plastid in a cell.
  • Usefulness: For tRNA researchers and those who are looking for new tRNA sequences, this database would be really useful. It can be used to compare tRNA sequences from different parts of a cell, and across species as well. In addition, if a researcher had a WT tRNA sequence and wanted to see how a mutation would impact the tRNA function, then they have a list of sequences and studies to review.
  • Timeliness: This database is needed to fill some gaps in tRNA research and to provide a more updated database that is well-curated and includes data coming from new scientific techniques. In the corresponding paper, the researchers note that while there are two older tRNA sequence databases, they both have some issues. The first database, tRNAdb, has not been updated since 2007 so all of the new sequencing data for tRNA that has been released since then is not in that database (Sajek et. al., 2020). The other database, GtRNAdb,uses genomic data to make predictions about the tRNA (Sajek et. al., 2020). However, the database does not check to see if those predictions line up with the literature and some of their predictions need to be validated through experimentation (Sajek et. al., 2020). The T-psi-C database not only uses sequences obtained from tRNA sequencing, but also gives the 3D structures of the molecules and can be updated frequently by the scientific community (Sajek et. al., 2020). Since tRNAs seem to play a role in human disease (ex. breast cancer, hearing loss, etc.), it is important for researchers to have an updated database with tRNA sequencing data (Sajek et. al., 2020).
  • Current:
    • Neither the website for the database nor the corresponding article have the date when the database first went online.
    • It is unclear how often the database is updated.
    • The exact date of the last update is unclear, but in the "About" section they note that it was last updated in 2019. Based on the "Statistics" section on the front page, it was probably updated on June 6, 2019.

General Utility of the Database

  • Other Database Links: There are links to other databases posted: Modomics (in the "About" section), Protein Data Bank (PDB) (PDB used to cross-reference database entries), and Taxonomy Browser(in database entries)
  • Browsing and Downloading:
    • Browsing: It is somewhat easy to browse through the database. There are many ways to search through the data. One could use modified or unmodified tRNA sequence data, secondary structure, or a a tRNA ID to find a tRNA they want to learn about. In addition, it also allows the user to search for the tRNA type they want to find, put in the organisms that they want tRNA sequence from, put in the coding amino acids, and put in the noncoding sequence. It also allows the user to filter out entries created by users. Users also have the option of searching the database using an unmodified BLAST sequence. Thus the most difficult aspect of the database is that if the user doesn't know what they are looking for, the search options are not very helpful.
    • Downloading: It is really easy to download the data, however the data file contains the sequence data for multiple tRNAs, not just sequence data the one that I'm looking for. The data in the database can be downloaded as a FASTA file (.fasta), an unmodified FASTA file (.fasta), as a CSV file (.csv), and as a dot-bracket file (.txt). These files either contain information about the sequence (.fasta) or the secondary structure (.txt). The CSV file contains all of the information that is found in the database entry. Since RNA is a nucleic acid and FASTA is commonly used for nucleic acid sequences, this database is using a standard file format to store its data.
  • User Friendliness: Overall, the database is not very friendly for naive users. One of the biggest difficulties with the database is that in order to perform a really meaningful search, the user should have the sequence of the tRNA or know something about the tRNA (ex. organism, type, anticodon sequence, etc.)
    • Organization: Overall, the website categories are well organized. It is easy to find the "About" section and to navigate through the site. However, more could be done to organize the results received after doing a search in the database so it is easier to go through the results.
    • User Assistance: While the database has an about section, it doesn't have a help section or any tutorials for naive users. Moreover, much of the about section is filled in technical information that a naive user would not understand.
    • Search Options: The variety of search options was overwhelming as naive user. Many of the search options could only be used if the user had information about the amino acid. The only search categories that could be helpful for naive users would be to search by the 3D model, tRNA type, and by who created the entry. But if the user doesn't know any of those things, the database is difficult to use. I can imagine it would be much more useful for researchers who know a lot about the tRNAs they are interested in.
    • Sample Query: In the database, I looked for tRNAs from humans (Homo sapiens). The database does not give me the number of results I got, but there are 7 pages of results so there are a lot of results. It is difficult to make sense of the results because the search results only returned a large table with the tRNA ID for each amino acid, and the other tables (coding AA, anticodon sequence, organism, type, etc.) do not do enough to differentiate results for the naive user. However, the results did show me all of the tRNAs that were found in humans so the results were accurate considering what I searched.
  • Access: The main restriction on access relates to uploading data. In order for users to upload data, they need to create an account on the website and follow the relevant protocols. However, anyone can look through the database and any member of the scientific community can follow the steps to create an account and update the database.

Summary Judgement

  • Overall, I would not recommend that a person unfamiliar with tRNA to use this database. It is difficult to find the tRNA that you are looking for if you don't already have a good amount of information on it. In addition, the results and download function of the database should be reworked to be more specific and easier to use for naive users. However, a tRNA researcher would find this database very useful, and I would recommend it to them.
  • Even through the database staff is associated with the Polish National Academy, the database is more of a "hobby" database. It is maintained by a small group of people and the database is limited in scope because it only covers a tRNA sequences.

Conclusion

From this activity, it is clear that the T-psi-C database, while not great for naive users, offers a great variety of information for tRNA researchers.

Acknowledgements

I copied and modified the assignment from the Week 10 assignment page to complete the sections. I used the NAR article about my database to answer questions about the scientific quality. I also went to the database site directly to learn more about the functionality of the site. Except for what is noted above, this individual journal entry was completed by me and not copied from another source Carolyne (talk) 23:51, 1 April 2020 (PDT)

References

  • Sajek, M. P., Woźniak, T., Sprinzl, M., Jaruzelska, J., & Barciszewski, J. (2019). T-psi-C: user friendly database of tRNA sequences and structures. Nucleic Acids Research, 48(D1), D256-D260. doi:10.1093/nar/gkz922
  • OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved March 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10

User Page and Template Links

Individual Journal Pages

  1. Carolyne week 2
  2. Carolyne week 3
  3. Carolyne week 4
  4. Carolyne week 5
  5. Carolyne week 6
  6. Carolyne week 8
  7. Carolyne week 9
  8. Carolyne week 10
  9. Carolyne week 11
  10. Carolyne week 13
  11. Carolyne week 14

Weekly Assignments

  1. BIOL368/S20:Week 1
  2. BIOL368/S20:Week 2
  3. BIOL368/S20:Week 3
  4. BIOL368/S20:Week 4
  5. BIOL368/S20:Week 5
  6. BIOL368/S20:Week 6
  7. BIOL368/S20:Week 8
  8. BIOL368/S20:Week 9
  9. BIOL368/S20:Week 10
  10. BIOL368/S20:Week 11
  11. BIOL368/S20:Week 13
  12. BIOL368/S20:Week 14

Class Journal Pages

  1. BIOL368/S20:Class Journal Week 1
  2. BIOL368/S20:Class Journal Week 2
  3. BIOL368/S20:Class Journal Week 3
  4. BIOL368/S20:Class Journal Week 4
  5. BIOL368/S20:Class Journal Week 5
  6. BIOL368/S20:Class Journal Week 6
  7. BIOL368/S20:Class Journal Week 8
  8. BIOL368/S20:Class Journal Week 9
  9. BIOL368/S20:Class Journal Week 10
  10. BIOL368/S20:Class Journal Week 11
  11. BIOL368/S20:Class Journal Week 13
  12. BIOL368/S20:Class Journal Week 14
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