DrugCentral Week 5

DrugCentral (Online drug Compendium)

General information about the database

1. What is the name of the database? (link to the home page)
   • DrugCentral from the homepage: http://drugcentral.org/
2. What type (or types) of database is it?
   • This database is for drug information, including active ingredients that are FDA approved.
3. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
   • This database contains information provides three different ways to search, by Drug, Target, and Pharmological action. For example, as stated by the website, "A comprehensive list of drug development codes and salt or ester forms are also stored in the database." (http://drugcentral.org/) It also contains the molecular structure of the drug, properties, and usage of the drug, etc.
4. What type of data source does it have?
   • primary versus secondary ("meta")?
     • - Secondary
   • curated versus non-curated? If curated, is it electronic versus human curation? If human curation, is it in-house staff versus community curation?
     • Human curation - in-house staff.
       • "Database developed and maintained by Oleg Ursu and Tudor Oprea. Web application developed by Jayme Holmes." (DrugCentral.org)

1. What individual or organization maintains the database?
   • public versus private?
     • Public
   • large national or multinational entity or small lab group?
     • Division of Translational Informatics at University of New Mexico in conjuction with the IDG (Illuminating the Druggable Genome)
2. What is their funding source(s)?
   • The National Institute of Health

Scientific quality of the database

1. Does the content appear to completely cover its content domain?
   • Yes, the database claims to have drug information available for the general public by integrating the structure and pharmacologic actions made by the FDA approved ingredients. The content is described in detail when searching drug names.
2. How many records does the database contain?
   • This database has 97,271 pharmaceutical formulations with FDA approved labels.
3. What claims do the database owners make about coverage in the corresponding paper?
   • It states to have limited information on discontinued drugs and those approved outside the US.
4. What species are covered in the database? (If it is a very long list, summarize.)
   • In the updates 2018 version there are 11,241 human proteins and 4,240 other species entities.
5. Is the database content useful? I.e., what biological questions can it be used to answer?
   • Yes, it can answer the biological questions of what pharmaceutical drugs are best effective for different illness, symptoms, and conditions.
6. Is the database content timely?
   • Yes, it being available for the public is important for patients to be aware of the drugs they are taking.
7. Is there a need in the scientific community for such a database at this time?
   • Yes, scientists and scientific writers are able to refer to this information for further research and developments in drug use.
8. Is the content covered by other databases already?
   • Information on the DrugCentral article was cited from 21 outside sources.
9. How current is the database?
   • The latest update was made within the last year.
10. When did the database first go online?
    • It was first made public in 2016.
11. How often is the database updated?
    • For the past three years it has been updated twice.
12. When was the last update?
    • In 2018 and was a part of the Nucleic Acids Research Journal Volume 47, Issue D1, released on January 8, 2019

General utility of the database to the scientific community

1. Are there links to other databases? Which ones?
   • Yes, The ChEMBL, PubChem, Pharos, Probes & Drugs portal, and SCI Data.
2. Is it convenient to browse the data?
   • Yes, it holds a great amount of information on drugs
3. Is it convenient to download the data?
   • It is convenient to download on a public computer, however a private computer would have a lot of storage taken up since the file is large.
4. In what file formats are the data provided?
   • A .sdf.gz file form where .sdf is for molecular structuring and .gz is a compresses archive file
5. What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
   • .gz and .sdf file types
6. Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
   • Standard formats. This database has bar graphs and pie charts that summarize its information. It also has the name of the drug next to its definition and a structural representation of its makeup.
7. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
   • Yes, the information can easily be accessed by the indicated search tab on the top of the page
8. Is the website well-organized?
   • Yes, everything is well labeled.
9. Does it have a help section or tutorial?
   • No, instead it has a About section that gives information on how and where the resources are created
10. Are the search options sensible?
    • There is a single search option on the top of the page that can lead to results involving drug, target, and disease.

Run a sample query. Do the results make sense?

• While attempting to create a query via Access, the SQL files would not download properly and would fail to open. There was no option to change the file name from .sql or .zip --> .txt.

1. Access: Is there a license agreement or any restrictions on access to the database?
   • The information is under the Creative Commons License

Summary judgment

1. Would you direct a colleague unfamiliar with the field to use it?
   • Yes, especially when knowing a drug name or what target the colleague is trying to get information on .
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.
   • This is a professional database funded by the National Institute of Health and approved using FDA regulated drugs.

Presentation File:DrugCentral Presentation.pptx

References

DrugCentral. Retrieved September 30, 2019 from http://drugcentral.org

Acknowledgements

This week I worked with User:Ntesfaio and User:Knguye66 on the Biological Databases individual journal and presentation. We received approval and instructional help from Dr. Dahlquist User:Kdahlquist.

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

Template:Ntesfaio Template:Knguye66 Knguye66 (talk) 21:41, 30 September 2019 (PDT) Ntesfaio (talk) 21:42, 30 September 2019 (PDT)