Isai Lopez Individual Journal 14
From OpenWetWare
Jump to navigationJump to search
Part 1: Individual In-Class Assignment
- What database did you access? (link to the home page of the database)
- I accessed the SIDER Database of Drugs and Side Effects
- http://sideeffects.embl.de/
- What is the purpose of the database?
- The database is meant to disperse information on known side effects of drugs. The information is collated by purpose of the drug and organ system it is meant to treat problems of.
- http://sideeffects.embl.de/about/
- What biological information does it contain?
- The website provides a chemical structure of the molecule, as well as frequencies of the most reported side effects associated with the drugs. In addition, the database provides links to other databases such as PubChem the provide additional background information on the drug. Even more, there are links to labels provided by the FDA on the drugs, their specific side effects, frequencies, and other safety information.
- http://sideeffects.embl.de/drugs/2099/?
- What species are covered in the database?
- In addition to humans, other species covered by the database include guinea pigs, rats, mice, as well as dogs, most likely due to testing of the drug prior to clinical trials. A total of 1430 drugs are listed in the database.
- http://sideeffects.embl.de/labels/dpdonline/kN8Jmyq+oE8=/C0043352/
- What biological questions can it be used to answer?
- What are the known side effects of the drug and are there any alternatives that would be more beneficial or safe for a patient to take? What other drugs will interact with this specific drug to create a potentially dangerous interaction? Also, what proteins in the human body do these drugs interact with and how can we take advantage of these interactions to tailor drug prescription to a person's specific condition and sensitivities?
- http://stitch.embl.de/cgi/network.pl?taskId=H3LUfRtPhF6S
- What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
- The database is a specialty database centered around label information reported by drug manufacturing companies curated electronically.
- What individual or organization maintains the database?
- It seems that the database is maintained, or was at least created, by four people: Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702794/
- What is their funding source(s)?
- The database is funded by a number of organizations, including Novo Nordisk Foundation, European Molecular Biology Laboratory (EMBL), and possibly GmbH.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702794/
- Is there a license agreement or any restrictions on access to the database?
- The database is licensed under Attribution-NonCommercial-ShareAlike 4.0 International. Under this agreement, the only restriction are use for commercial purposes, attribution of information, and that any contribution of data using this database has to be distributed under the same license.
- https://creativecommons.org/licenses/by-nc-sa/4.0/
- How often is the database updated? When was the last update?
- The most current version (SIDER 4.1) was released on October 21, 2015. From what I could find on the website, it does not appear to have been updated since then.
- http://sideeffects.embl.de/
- Are there links to other databases?
- Yes, there are links to plenty of other databases including: PubMed and STITCH
- https://pubchem.ncbi.nlm.nih.gov/
- http://stitch.embl.de/cgi/
- Can the information be downloaded? And in what file formats?
- Yes, there is a download tab that allows the user to download the current version of SIDER 4.1. The files are formatted in tsv.gz format, which is a compressed archive file extension.
- http://sideeffects.embl.de/download/
- Evaluate the “user-friendliness” of the database.
- Is the Web site well-organized?
- Yes, there are few tabs to navigate through, and drugs are organized by purpose. Side effects are organized by name in alphabetical order. If you cannot find a drug using the "Drug List" tab, you can type it in the search bar and find it that way. My issue with the search bar is that it requires you to know the generic name, and not a brand name. For example, "Advil" is not recognized but "Ibuprofen" is.
- Does it have a help section or tutorial?
- No tutorial on the site, but many of the terms or labels on the pages have a little circle that you can hover hover for more detailed information.
- Run a sample query. Do the results make sense?
- I ran a query on the drug epinephrine, and a list of side effects are listed. The list seems to make sense, but little information is given. For example, under the first side effect "Lactic acidosis", all boxes are grayed out, meaning not frequency information was reported to SIDER. As such, not much information can be learned in terms of frequencies of side effect occurrences. The boxes correspond to the labels reported by sources of information, which can be useful for learning more.
- Is the Web site well-organized?
Acknowledgments
- This was an individual in-class assignment, so all work was completed without outside help.
- Isai Lopez 18:41, 22 November 2016 (EST):
- I used the wiki syntax for the questions from the Week 14 Assignment Page provided by Dr. Dahlquist
- I worked with Anindita Varshneya, Shivum A Desai, and Will Fuchs both in class in the writing of our outline as well as the revision of the powerpoint as well as out of class on several occasions.
- While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
References
- Week 14 Assignment Page
- SIDER Database Website
- See Anu Week 14 Individual Journal Page for our group assignment.
