Jordan T. Detamore Week 14
Part 1: Biological Databases
The purpose of the assignment was to learn about many different types of databases and explore a specific database in order to teach the class about it.
- What database did you access? (link to the home page of the database)
- What is the purpose of the database?
- The purpose of the database is to provide information about the genomics of rice by curating a collection of information from many different community sources IC4R Overview
- What biological information does it contain?
- There is summary information, genome context, gene browser, transcripts information, expression level, homolog group, SNP variation information, post-translational modification, gene related literature, additional links to other functional annotation and sequences of genes of interest in rice IC4R Tutorial
- What species are covered in the database?
- Rice (Oryza sativa) Information Commons for Rice
- What biological questions can it be used to answer?
- Questions relating to the genome of rice can be answered using this database Information Commons for Rice
- 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 is a model organism database, is meta, and is curated manually in-house Information Commons for Rice
- What individual or organization maintains the database?
- A committee of people from the Beijing Institute of Genomics, China Agricultural University, Peking University, Huazhong University of Science and Technology, and Huazhong Agricultural University Commitee and Advisory Board
- What is their funding source(s)?
- Strategic Priority Research Program of the Chinese Academy of Sciences
- National Programs for High Technology Research and Development
- Is there a license agreement or any restrictions on access to the database?
- There is no restriction to access to the database. Anybody can go to the website and access the information IC4R Terms
- How often is the database updated? When was the last update?
- The website does not say how often it is updated but it was last updated on May 5, 2016
- Are there links to other databases?
- Can the information be downloaded? And in what file formats?
- Information can be downloaded in .fasta and .pdf formats 
- Evaluate the “user-friendliness” of the database.
- Is the Web site well-organized?
- Yes you can navigate all aspects of the site from the homepage Information Commons for Rice
- Does it have a help section or tutorial?
- Yes it has both a help section and tutorial Information Commons for Rice
- Run a sample query. Do the results make sense?
- Yes it provides examples of things to search and you can search by organism, ontology, or sequence Search Tap
- Is the Web site well-organized?
I learned a lot about IC4R which is a database that tells you everything you need to know about the genome of rice. It was a very direct and accessible database that could be used by scientists of all experiences. I learned a lot about databases in general and am interested to hear my classmates present on their databases.
- I received instruction from Dr. Dahlquist's in class
- While I worked with the person noted above, this individual journal entry was completed by me and not copied from another source.
- Jordan T. Detamore 16:41, 22 November 2016 (EST):
Joint Page: Courtney L. Merriam Week 14
Edited ppt: Schade Journal Club Part I
Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356