Mpaniag1 Week 10

Purpose

The purpose of this lab is to review and critique the database of our choice to provide information to our colleagues about its quality and utility when doing scientific research.

Questions

General information about the database

1. What is the name of the database? PathBank, https://pathbank.org/
2. What type (or types) of database is it? pathways found in model organisms,i. Metabolite/Compound pathways ii. Protein Pathways-Protein sequence database (https://academic.oup.com/nar/article/48/D1/D470/5585552)

• 1. 1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])-metabolite/compound and protein pathways found in model organisms (https://academic.oup.com/nar/article/48/D1/D470/5585552)
     2. What type of data source does it have?
        • primary versus secondary ("meta")?- Secondary (https://academic.oup.com/nar/article/48/D1/D470/5585552)
        • curated versus non-curated?- Curated(https://academic.oup.com/nar/article/48/D1/D470/5585552)
          • if curated, is it electronic versus human curation? Human (https://academic.oup.com/nar/article/48/D1/D470/5585552)
            • if human curation, is it in-house staff versus community curation? In House Staff (https://academic.oup.com/nar/article/48/D1/D470/5585552)
  2. What individual or organization maintains the database?
     • public versus private-Public
     • large national or multinational entity or small lab group-Supported by Dr. David Wishart of the Departments of Computing Science & Biological Sciences at the University of Alberta/Wishart Research Group (https://pathbank.org/about)
  3. What is their funding source(s)? Canadian Institutes for Health Research (CIHR); Canada Foundation for Innovation, Major Science Initiatives Fund (CFI-MSI); Genome Alberta (a division of Genome Canada). Funding for open access charges: Genome Alberta (https://academic.oup.com/nar/article/48/D1/D470/5585552)

Scientific quality of the database

• 1. Does the content appear to completely cover its content domain?
     • How many records does the database contain?- 78, 488 different compounds (including metabolites, drugs and other xenobiotics), 8,993 different proteins and describes more than 176 535 different reactions and interactions and 109,836 Metabolite/Compound pathways and 398 Protein pathways (https://academic.oup.com/nar/article/48/D1/D470/5585552)
     • What claims do the database owners make about coverage in the corresponding paper?-Author states, limitations include there are significantly fewer protein pathways compared to metabolism because the curation team focused on metabolism in the beginning stages of PathBank, only 10 Model organisms available at the moment, plan to introduce 9 more within the next two years, limited analytical tools (https://academic.oup.com/nar/article/48/D1/D470/5585552)
  2. What species are covered in the database? (If it is a very long list, summarize.)-10 model organisms, (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli and Pseudomonas aeruginosa) (https://academic.oup.com/nar/article/48/D1/D470/5585552)
  3. Is the database content useful? I.e., what biological questions can it be used to answer?- Yes, this database's content is useful, it answers the biological question of what function does this molecule have in a pathway?
  4. Is the database content timely?
     • Is there a need in the scientific community for such a database at this time?- As a student, I believe this type of database is needed to organize scientific pathways in order to make connections
     • Is the content covered by other databases already?- Other databases do cover metabolic and protein pathways (https://academic.oup.com/nar/article/48/D1/D470/5585552)
  5. How current is the database?
     • When did the database first go online?-Not stated, found images that were created in 2013, but there was no official data for when the database first went online(https://pathbank.org/view/SMP0000343)
     • How often is the database updated?- Not stated
     • When was the last update?-August 2019 (https://academic.oup.com/nar/article/48/D1/D470/5585552)

General utility of the database to the scientific community

• 1. Are there links to other databases? Which ones?- Yes, HMDB, UniProt, and DrugBank (https://pathbank.org/)
  2. Is it convenient to browse the data?-No, a lot of information, if you conduct a search, results obtained are in random order with sometimes 100s of pages of possible pathways'
  3. Is it convenient to download the data?- Yes
     • In what file formats are the data provided?
       • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? -.png,.svg, simple .svg, large_font.svg, Simple_Large_font.svg, greyscale .svg, .owl, .sbgn, .sbml, and all files .zip
       • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?- The database is providing standard formats for pictures of the pathways
  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?-No, when I looked up a specific enzyme I got 96 pages of results, I did not know what order this information was in and how to go about looking for a specific pathway. (https://pathbank.org/search?species_name=Homo+sapiens&q=cyclase&subject=Metabolite&metabolite_category=&protein_category=)
     • Does it have a help section or tutorial?- Not directly on the page, but the article provides instructions on how to carry out a search. (https://academic.oup.com/nar/article/48/D1/D470/5585552)
     • Are the search options sensible?- Yes, the search options are sensible but limited
     • Run a sample query. Do the results make sense?- Yes the results made sense, search cyclase, in homo sapiens, in metabolic pathways, but got 96 results all of which included the enzyme cyclase. (https://pathbank.org/search?species_name=Homo+sapiens&q=cyclase&subject=Metabolite&metabolite_category=&protein_category=)
  5. Access: Is there a license agreement or any restrictions on access to the database?- Made available through the Open Database License (https://pathbank.org/)
• Summary judgment
  1. Would you direct a colleague unfamiliar with the field to use it?-Yes and No, because if a colleague has never learned about metabolic and protein pathways, this is a great way to get a visual, but they would need to know the specifics of the pathway they were trying to get a visual for
  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.- I think it was meant to be a professional database. It is fairly well organized, has a good amount of data for the 10 model organisms and according to the article the creators had hopes of expanding, but that being said the last edit was made in 2019.

Conclusion

The science conducted this week was database analysis. In conclusion, this week's lab exposed me to the thousands of different databases that exist, and with the questions asked gave me a good idea on how to evaluate the database. In addition, I learned to navigate a new database that I can use in further scientific research.

Acknowledgements

• I copied and modified the protocol shown in the Week 10 page
• Except for what is noted above, this individual journal entry was completed by me and not copied from another source

Mpaniag1 (talk) 18:18, 1 April 2020 (PDT)

References

• OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved March 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10
• PathBank. (n.d.). Retrieved March 26, 2020, from https://pathbank.org/
• Wishart, D. S., Li, C., Marcu, A., Badran, H., Pon, A., Budinski, Z., … Ramirez-Gaona, M. (2019). PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Research, 48(D1). doi: 10.1093/nar/gkz861

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