CGDB: Circadian Gene DataBase

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CGDB: Circadian Gene DataBase

General Information

  1. CGDB: Circadian Gene DataBase
  2. This is a circadian gene database.
    1. The database includes circadian gene DNA and protein sequences, model organisms specific to each circadian gene, clear descriptions of the circadian gene functions, and circadian gene tags specific to this database and other databases (http://cgdb.biocuckoo.org/view.php?id=021036).
    2. Circadian Gene DataBase is a secondary source of data.
  3. The Cuckoo Workgroup Maintains the database.
  4. This organization is funded by:

Quality of Science

  1. Content Domain:
  2. The species covered in the database include plants, animals, and fungi (http://cgdb.biocuckoo.org/browse.php).
  3. Is the database content timely?

General Utility

  1. Are there links to other databases?
  2. Is it convenient to browse the data?
    • The data is fairly convenient to browse.
  3. Is it convenient to download the data?
    • The convenience of data depends on your preference. When downloading the data a new browser tab is opened with all of the protein sequences listed for each gene which is fairly easy to read. The only con is that you will have to copy and paste the data into another file to store it.
    • All downloads come in the .txt format (http://cgdb.biocuckoo.org/download.php).
    • A TXT file is a standard text document and does not have any formatted text (https://fileinfo.com/extension/txt).
  4. ”User Friendliness” of the website:
      • Although the website is not especially visually pleasing, it is rather straight forward to navigate.
      • The website contains a user guide which is easy to find and very straight forward.
      • The search options are fairly sensible. It is possible to run a search query with broad keywords of species or genes in order to find what you are looking for, however a knowledge of what you are looking for is definitely required.
      • When running a sample query of the keyword “human,” all of the genes with the homo sapiens tag show up, with their unique identifiers that allows the user to browse through the sequences of the circadian genes related to homo sapiens. These results make sense.
  5. There is not a license agreement for this website, however there is an article that users must cite if they are publish the results found on the website.
    • The citation should read: CGDB: a database of circadian genes in eukaryotes Shujing Li, Ke Shui, Ying Zhang, Yongqiang Lv, Wankun Deng, Shahid Ullah, Luoying Zhang and Yu Xue. Nucleic Acids Res. 2016; 10.1093/nar/gkw1028.