Cdominguez Week 10

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Assignment Page Individual Journal Entries Class Journal
BIOL368/S20:Week 1 user:cdominguez BIOL368/S20:Class Journal Week 1
BIOL368/S20:Week 2 cdominguez Week 2 BIOL368/S20:Class Journal Week 2
BIOL368/S20:Week 3 cdominguez Week 3 BIOL368/S20:Class Journal Week 3
BIOL368/S20:Week 4 cdominguez Week 4 BIOL368/S20:Class Journal Week 4
BIOL368/S20:Week 5 cdominguez Week 5 BIOL368/S20:Class Journal Week 5
BIOL368/S20:Week 6 cdominguez Week 6 BIOL368/S20:Class Journal Week 6
BIOL368/S20:Week 8 cdominguez Week 8 BIOL368/S20:Bibliography
BIOL368/S20:Week 10 cdominguez Week 10 BIOL368/S20:Class Journal Week 10
BIOL368/S20:Week 11 cdominguez Week 11 BIOL368/S20:Class Journal Week 11
BIOL368/S20:Week 13 cdominguez Week 13 BIOL368/S20:Class Journal Week 13
BIOL368/S20:Week 14 cdominguez Week 14 BIOL368/S20:Class Journal Week 14

Purpose

To interact with a database in order to understand how to effectively gain scientific knowledge from it to actively work with the data and critically think through its analysis as scientists.

Questions

  • General information about the database
    1. What is the name of the database? [gutMDisorder Homepage]
    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?])This database contains sequence data about particular microbes that can cause disorders as well as intervention descriptions that can potentially alter the health and microbiota of those with disorders [Nucleic Acids Research]
      2. What type of data source does it have?
    3. What individual or organization maintains the database? Harbin Medical University [gutMDisorder Homepage]
    4. What is their funding source(s)? The Tou-Yan Innovation Team Program of the Heilongjiang Province, National Natural Science Foundation of China ,China Postdoctoral Science Foundation, Heilongjiang Province Postdoctoral Fund, Funding for open access charge: The Tou-Yan Innovation Team Program of the Heilongjiang Province, National Natural Science Foundation of China, China Postdoctoral Science Foundation, Heilongjiang Province Postdoctoral Fund [Nucleic Acids Research]
  • Scientific quality of the database
    1. Does the content appear to completely cover its content domain? The content appears to begin to cover its content domain. From browsing the database, it is only version 1 of this database and thus they only have their initial curation posted. This includes a more limited amount of disorders, drugs, foods, but a more extensive list of microbiota. However, it does seem like an organized way of starting to develop this type of database that has not been done before. [gutMDisorder Homepage]
      • How many records does the database contain? the website states that they have "2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse" [gutMDisorder Homepage]
      • What claims do the database owners make about coverage in the corresponding paper? Its claims are based on a comprehensive look at gut microbiota, intervention, and drugs. Its coverage is based on pre-existing papers that they found to have claims related to this and thus imported into this database. [Nucleic Acids Research]
    2. What species are covered in the database? (If it is a very long list, summarize.) Human and Mouse [gutMDisorder Homepage]
    3. Is the database content useful? The biological questions that could be answered are related to associations between the gut microbiota and diseases, intervention, and drugs. It bases this on data collected from mouse and human, which is definitely useful to be relatable to people who are looking to acquire information about this.
    4. Is the database content timely? Yes, this gives more information on associations that is not available elsewhere since this is the first database like it.
      • Is there a need in the scientific community for such a database at this time? I believe so. This can be helpful in the development of health related solutions to chronic diseases. Learning more about the associations between gut microbiota and diseases and connecting it to intervention with food and drugs can yield very useful associations between them.
      • Is the content covered by other databases already? No, it claims it is the first of its kind.
    5. How current is the database?
  • General utility of the database to the scientific community
    1. Are there links to other databases? Which ones? 'They are links to NCBI Taxonomy, Disease Ontology, and DrugBank [Resources]
    2. Is it convenient to browse the data? Yes, it is very convenient to browse the data. There are images with directions and flowchart on how to navigate the associations. The results are very straightforward and make it easy to go to the original paper in which they got the data from. [Browse]
    3. Is it convenient to download the data? Yes, on the homepage there is a link that directly downloads and open up on Excel. [Browse]
      • In what file formats are the data provided? Excel [gutMDisorder Homepage]
        • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? .xlsx
        • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? Standard
    4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?Yes, they give instructions to navigate it easily. [Browse]
      • Is the website well-organized? Yes. [Browse]
      • Does it have a help section or tutorial? When you go to browse or search the database, it automatically takes you to a flowchart before you start so that you can navigate how to correctly use the website. [Browse]
      • Are the search options sensible? Yes you are able to search for all the different categories such as microbiota, interventions, disorder, and species. [Browse]
      • Run a sample query. Do the results make sense? I did a search for human species and disorder of type 2 diabetes. This gave me a clear list of associations of a multitude of gut microbiota. When clicking on "details" of the first bacteria, it opens up a window that makes it easy to understand where this information came from and how the paper came to this conclusion. [gutMDisorder Type 1 Diabetes Search]
    5. Access: Is there a license agreement or any restrictions on access to the database? It is a part of Open Access. [Nucleic Acids Research]
  • Summary judgment
    1. Would you direct a colleague unfamiliar with the field to use it? Yes, it is fairly straightforward and provides a conclusion from the paper where the association is found. It is not wordy with too much scientific language and feel that it is a good database if one was looking into this particular topic.
    2. Is this a professional or "hobby" database? I think that this is a professional database that is at the beginning of its potential. It is limited in the amount of association it has however as it is based in a major national university, it still is professional in its setup.

Scientific Conclusion

This database allowed for an initial avenue into looking at possible associations between gut microbiota, interventions, and diseases. This is a database that can be very useful in looking for new ways to address certain diseases that impact the human population. Although it is clear that it is in its first version and in need of more extensive data, it is a good start to using available data to make more accessible connections to the public.

Acknowledgments

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

Cdominguez (talk) 15:04, 26 March 2020 (PDT)

References

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