Mia Huddleston Week 14
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Electronic Notebook
Purpose
The purpose of this lab is to analyze and explore a database of our choosing to look at what it holds and the database works. For the second portion of the lab, with the help of my partners, we created an outline based off of the Hebly et al. paper, found thirty definitions of words that we did not know, and fixed the errors found in a previous presentation.
Methods and Results
- What database did you access? (link to the home page of the database)
- Cancer Resource
- http://data-analysis.charite.de/care/
- What is the purpose of the database?
- This database holds drug-target relationships, protein, and mutation data all relating to cancer. This database makes it possible to analyze and explore this data.
- https://academic.oup.com/nar/article/44/D1/D932/2503093/CancerResource-updated-database-of-cancer-relevant
- What biological information does it contain?
- This database includes; compounds, cancer-relevant protein targets, compound-target interactions, cell lines, genes (mutations), mutations, and genes (expression) from cancer genomic experiments.
- http://data-analysis.charite.de/care/
- What species are covered in the database?
- There is only information for human drugs, genes, etc.
- http://data-analysis.charite.de/care/index.php
- What biological questions can it be used to answer?
- This database can be used to find drug-target interactions found in cancer experimental-data. You can also look for a specific drug or potential target for a drug.
- http://data-analysis.charite.de/care/index.php?site=about#cdb
- 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])?
- This database holds sequences of compounds, cancer-relevant protein targets, compound-target interactions, cell lines, genes (mutations), mutations, and genes (expression), and is in house.
- http://data-analysis.charite.de/care/
- What individual or organization maintains the database?
- The German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany is the institute that maintains the database.
- http://data-analysis.charite.de/care/index.php?site=contact
- What is their funding source(s)?
- The website looks to be open access to all and is funded by a University.
- http://data-analysis.charite.de/care/
- Is there a license agreement or any restrictions on access to the database?
- How often is the database updated? When was the last update?
- The last update was September 2015, which is quite a long time ago
- Are there links to other databases?
- Yes, they link to a couple of other databases in their link section.
- http://data-analysis.charite.de/care/index.php?site=links
- Can the information be downloaded? And in what file formats?
- It does not look like there is an easy way to download he information from this database.
- http://data-analysis.charite.de/care/index.php?site=about
- Evaluate the “user-friendliness” of the database.
- I think this database is very user friendly and easy to navigate. They are very clear on what you can find and where you can find it. They also are very good at giving you as much information on what you are looking for as possible.
- http://data-analysis.charite.de/care/index.php?site=search_target
- Is the Web site well-organized?
- I think the website is really well organized and very easy to organize. Especially with the different tabs of where to find what information.
- http://data-analysis.charite.de/care/index.php?site=drug_search_form
- Does it have a help section or tutorial?
- Yes, right on the home page it says how to find what you are looking for, there is also an FAQ section.
- http://data-analysis.charite.de/care/index.php
- http://data-analysis.charite.de/care/index.php?site=about
- Run a sample query. Do the results make sense?
- Yes, I am surprised by how much information they give and how organized it is. They list all the detailed information on the gene, the cancer relevant pathways in which the gene is involved in, an expression profile, mutation profile, and more.
- http://data-analysis.charite.de/care/index.php?site=search_target
Group Assignment
The group assignment is located on Matthew Oki's journal 14 page.
Acknowledgements
The group project portion was completed with my partners, Matthew Oki, Matthew R Allegretti, and Colin Wikholm, with meetings in class and outside of class on Sunday. I would also like to thank Kam D. Dahlquist, Ph.D. for the instruction in class. Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Mia Huddleston 15:07, 5 December 2016 (EST)
References
- Hebly, M., de Ridder, D., de Hulster, E. A. F., de la Torre Cortes, P., Pronk, J. T., & Daran-Lapujade, P. (2014). Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles. Applied and Environmental Microbiology, 80(14), 4433-4449. doi: 10.1128/AEM.00785-14
- Week 14 Assignment Page
Useful links
User Page: Mia Huddleston
Bioinfomatics Lab: Fall 2016
Class Page: Bioinfomatics Laboratory, Fall 2016
