DrugComboDB Review

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Purpose

The purpose of this lab is to familiarize ourselves with navigating databases. Databases can have a variety of features, and these features can be analyzed to better understand how a database can be created and maintained. Through analysis of the DrugComboDB, we can better discover these components and apply them to future databases we visit.

Database Evaluation

  • This information was copied from Anna Horvath's Week 8 page. The history is available on that page.
  • 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 website, this database integrates drug combinations from different sources. It has 2,887 single drugs and 448,555 combinations. It is the first comprehensive database and has the largest number of drug combinations. The purpose is to determine whether drugs work synergistically or antagonistically to one another.
      1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
        • The data it contains is screened assays of drugs, looking specifically at drug targets and mechanisms of action.
      2. What type of data source does it have?
        • primary versus secondary ("meta")?
          • This source has secondary data. It takes from screened assays of drug combinations, external databases, and from PubMed literature.
        • curated versus non-curated?
          • if curated, is it electronic versus human curation?
            • This website is human-curated, as noted on the main page of the website. They state that computed the scores determining the synergy or antagonism of the drugs. They also prepared the models of the database.
            • if human curation, is it in-house staff versus community curation?
              • This was curated through in-house staff, as they state within their article that the authors created the different components of the website, including the ‘search’, ‘filtering’, ‘graphical visualization’ and ‘download’ modules.
    3. What individual or organization maintains the database?
      • This is a professional database maintained by Changzhou University & CSU. It does not allow community contribution, the authors continually maintain it.
      • public versus private
      • large national or multinational entity or small lab group
        • The database is run by the lab group mentioned above in Changzhou University, which is located in Jiangsu, China.
    4. What is their funding source(s)?
  • Scientific quality of the database
    1. Does the content appear to completely cover its content domain?
      • The content within the database appears to have a very large variety of drugs uploaded. These drugs are many of those that affect the brain, lung, liver, hematopoietic/lymphoid, kidney, ovary, uterus, rectum, breast, skin, colon, bone, and prostate. However, while all of the drugs available can be combined to determine their effects on one another, they likely do not have all drugs in the database. This is because they do not have certain common drugs, such as acetaminophen.
      • How many records does the database contain?
        • The database has 2,887 single drugs, 448, 555 combinations, 6,055,926 combination tests, and 124 cell lines according to their main page.
      • What claims do the database owners make about coverage in the corresponding paper?
        • The database owners state that their current drug combinations offered within the databases are limited in function because of their small sizes in comparison to the number of drugs out there. However, they state that they have a large amount of data on both experimental and well-documented, common drug combinations.
    2. What species are covered in the database? (If it is a very long list, summarize.)
      • The database has a long list of drugs offered, and these range in their types. The drugs listed are many of those that affect the brain, lung, liver, hematopoietic/lymphoid, kidney, ovary, uterus, rectum, breast, skin, colon, bone, and prostate. There are 2,887 total drugs on this database, so the list is extensive.
    3. Is the database content useful? I.e., what biological questions can it be used to answer?
      • The database content is incredibly useful because it can tell an individual whether the combinations of drugs that they have to use for a variety of illnesses can work either synergistically or antagonistically to one another. This is important because if two drugs taken have antagonistic effects, they have the potential to harm the individual taking them.
    4. Is the database content timely?
      • The database content appears to be timely. The authors of the paper state that since the website's release in December 2018, there have been a lot of visitors. The paper published on the website came out in January of 2020, so it is likely that they have earned even more attention since then.
      • 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 because the website has the ability to tell whether the combination of drugs an individual is using for a variety of illnesses work either synergistically or antagonistically to one another. This can be very helpful in the modern age, when there are a very large variety of drugs available for each illness. These drugs can have similar or very different effects and thus it is important to monitor these interactions.
      • Is the content covered by other databases already?
        • The content is not covered by other databases. They stated that to the best of their knowledge, DrugCombDB is the first comprehensive database. They state that it has the largest number of drug combinations to date.
    5. How current is the database?
      • This database is relatively current. They do not state when the database has been updated, however, it was published at the end of 2018, meaning it is relatively current.
      • When did the database first go online?
      • How often is the database updated?
        • The database does not state how often updates occur. This means that it could be updated weekly, monthly, or perhaps even yearly. The only indication of dates is on their 'Downloads' page.
      • When was the last update?
        • The last update was published on May 31st, 2019, according to the 'Downloads' page.
  • General utility of the database to the scientific community
    1. Are there links to other databases? Which ones?
      • There are links to other databases including PubMed and FDA
    2. Is it convenient to browse the data?
      • The data is easily accessible. It's also convenient as it's easy to find and download data sets as an excel document. Further, you could find Combinations for the drugs in the database by inputting its name.
    3. Is it convenient to download the data?
      • In what file formats are the data provided?
        • The formats that the data is provided in excel.
      • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
        • the files indicated by the file extension are .CSV, .xlsx, and .rar [1]
        • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
          • base on our analysis of the database, the files are using non-standard formats.
    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?
        • The website is well-organized. It's divided into sections that easily navigated. Also, each section is organized into subsections which makes it easy to navigate too.
      • Does it have a help section or tutorial?
        • The website has a tutorial section that's helpful.
      • Are the search options sensible?
        • The search options are sensible, they are not overwhelming, and are sufficient for gaining the amount of information needed.
      • Run a sample query. Do the results make sense?
        • The results do make sense, it goes along with literature.
    5. Access: Is there a license agreement or any restrictions on access to the database?
      • There's no license agreement or any restrictions on access to the database, the database could easily be found on google.
  • Summary judgment
    1. Would you direct a colleague unfamiliar with the field to use it?
      • I wouldn't direct a colleague unfamiliar with the field to use this database as it uses scientific terms that could be hard to understand which are shown in the search.
    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 as we both look forward to having careers in healthcare, we found this database to be a unique database as it analyzes the effects of drugs, therefore we believe that it's potentially very useful.

Scientific Conclusion

This week taught us to inspect the DrugComboDB database and understand its various components, including what data sources it has, who creates and maintains the database, and how valuable the information within the database is. Now, when we encounter databases as a scientist, we will be able to successfully navigate through them and decide whether the information we are being presented is valid

Acknowledgements

  • This page was created in collaboration by Anna Horvath and Fatimah Alghanem.
  • I, Anna, contacted my TA, Annika Dinulos, to ask about the acknowledgments section.
  • We copied and modified procedures from the Week 8 assignment page.
  • We used DrugComboDB as our database for this project.
  • We referred to the paper "DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy" for reference for our database.
  • Except for what is noted above, this individual journal entry was completed by Anna Horvath and Fatimah Alghanem and not copied from another source.

Anna Horvath (talk) 16:59, 28 October 2020 (PDT) Falghane (talk) 18:40, 28 October 2020 (PDT)

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