Difference between revisions of "CGDB: Circadian Gene DataBase"

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===References===
 
===References===
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#[http://cgdb.biocuckoo.org/ http://cgdb.biocuckoo.org/]
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#[http://cgdb.biocuckoo.org/view.php?id=021036 http://cgdb.biocuckoo.org/view.php?id=021036]
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#[https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes]
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#[http://www.biocuckoo.org/people.php http://www.biocuckoo.org/people.php]
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#[http://cgdb.biocuckoo.org/index.php http://cgdb.biocuckoo.org/index.php]
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#[http://cgdb.biocuckoo.org/browse.php http://cgdb.biocuckoo.org/browse.php]
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#[https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539 https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539]
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#[http://circadb.hogeneschlab.org/ http://circadb.hogeneschlab.org/]
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#[http://www.wgpembroke.com/shiny/SCNseq/ http://www.wgpembroke.com/shiny/SCNseq/]
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#[https://www3.nd.edu/~bioclock/ https://www3.nd.edu/~bioclock/]
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#[http://circadiomics.igb.uci.edu/ http://circadiomics.igb.uci.edu/]
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#[http://diurnal.mocklerlab.org/ http://diurnal.mocklerlab.org/]
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#[http://www.bioinfo.mpg.de/euclis/ http://www.bioinfo.mpg.de/euclis/]
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#[http://www.dbcryptochrome.org/ http://www.dbcryptochrome.org/]
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#[http://www.ensembl.org/index.html http://www.ensembl.org/index.html]
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#[http://cgdb.biocuckoo.org/links.php http://cgdb.biocuckoo.org/links.php]
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#[https://fileinfo.com/extension/txt https://fileinfo.com/extension/txt]
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#[http://cgdb.biocuckoo.org/download.php http://cgdb.biocuckoo.org/download.php]
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#[http://cgdb.biocuckoo.org/faq.php http://cgdb.biocuckoo.org/faq.php]
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#[http://cgdb.biocuckoo.org/advance.php http://cgdb.biocuckoo.org/advance.php]
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#[http://cgdb.biocuckoo.org/result.php?type=simple&page=1 http://cgdb.biocuckoo.org/result.php?type=simple&page=1]
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#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.

Revision as of 00:31, 2 October 2017

CGDB: Circadian Gene DataBase

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 (Info found here: 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 ( Info found here: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?
  3. Is it convenient to download the data?
  4. ”User Friendliness” of the website:
      • Although the website is not especially visually pleasing, it is rather straight forward to navigate.(Info found here:http://cgdb.biocuckoo.org/faq.php)
      • The website contains a user guide which is easy to find and very straight forward.(Info found here:http://cgdb.biocuckoo.org/faq.php)
      • 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.(Info found here:http://cgdb.biocuckoo.org/advance.php)
      • 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.(Info found here:http://cgdb.biocuckoo.org/result.php?type=simple&page=1)
  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. (Info found here:http://cgdb.biocuckoo.org/index.php)
    • 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.

Summary Judgement

  1. We would direct a colleague unfamiliar with the field to use this database. It contains interesting information that is easily accessible.
  2. This is a professional database.


Acknowledgements

  1. Simon and Hayden worked together in person and over text multiple times to complete this assignment.
  2. Simon and Hayden utilized the CGDB: Circadian Gene DataBase to complete the requirements for this assignment.
  3. Simon and Hayden also used the Week 5 assignment page to make sure the assignment requirements were fulfilled.


References

  1. http://cgdb.biocuckoo.org/
  2. http://cgdb.biocuckoo.org/view.php?id=021036
  3. https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes
  4. http://www.biocuckoo.org/people.php
  5. http://cgdb.biocuckoo.org/index.php
  6. http://cgdb.biocuckoo.org/browse.php
  7. https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539
  8. http://circadb.hogeneschlab.org/
  9. http://www.wgpembroke.com/shiny/SCNseq/
  10. https://www3.nd.edu/~bioclock/
  11. http://circadiomics.igb.uci.edu/
  12. http://diurnal.mocklerlab.org/
  13. http://www.bioinfo.mpg.de/euclis/
  14. http://www.dbcryptochrome.org/
  15. http://www.ensembl.org/index.html
  16. http://cgdb.biocuckoo.org/links.php
  17. https://fileinfo.com/extension/txt
  18. http://cgdb.biocuckoo.org/download.php
  19. http://cgdb.biocuckoo.org/faq.php
  20. http://cgdb.biocuckoo.org/advance.php
  21. http://cgdb.biocuckoo.org/result.php?type=simple&page=1
  22. 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.