Difference between revisions of "CGDB: Circadian Gene DataBase"

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.
      • The data has been curated.
      • The database utilizes human curation.
      • The database utilizes in house staff.
      • Info found here:https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes.
3. The Cuckoo Workgroup Maintains the database.
   • This is a private organization.
   • This organization consists of a small lab group.
   • Info found here:http://www.biocuckoo.org/people.php.
4. This organization is funded by:
   • National Basic Research Program
   • Natural Science Foundation of China
   • International Science & Technology Cooperation Program of China
   • Natural Science Foundation of Anhui Province
   • National Natural Science Foundation of China
   • Info found here: https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes.

Quality of Science

1. Content Domain:
   • The database contains over 72,800 experimentally verified genes with rhythmic expression (Info found here:http://cgdb.biocuckoo.org/index.php).
   • The database owners point out that there is a lack of comprehensive database which cycle genes across phyla and these owners claim to fill that need (Info found here:https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes).
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?
   • There is a need in the scientific community for this database at this time due to the fact that disruptions in circadian rhythms have been possibly entwined with diseases and disorders such as but not limited to psychiatric disorders and cancer. (Info found here: https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539)
   • This content is covered by other databases already, but not a comprehensive database for the circadian genes across phyla. (Info found here: https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539)
   • The database first went online in 2004. (Info found here: https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539)
   • The database is updated when new cycling genes are experimentally characterized. It appears that the database is updated monthly. (Info found here: https://academic.oup.com/nar/article/45/D1/D397/2333922/CGDB-a-database-of-circadian-genes-in-eukaryotes#51198539
   • The database was last updated October 1, 2017. (Info found here: http://cgdb.biocuckoo.org/index.php)

General Utility

1. Are there links to other databases?
   • This database contains links to other databases:
   • http://circadb.hogeneschlab.org/
   • http://www.wgpembroke.com/shiny/SCNseq/
   • https://www3.nd.edu/~bioclock/
   • http://circadiomics.igb.uci.edu/
   • http://diurnal.mocklerlab.org/
   • http://www.bioinfo.mpg.de/euclis/
   • http://www.dbcryptochrome.org/
   • http://www.ensembl.org/index.html
   • Important note: not all of these links are successful(Info found here: http://cgdb.biocuckoo.org/links.php
2. Is it convenient to browse the data?
   • The data is fairly convenient to browse. (Info found here:http://cgdb.biocuckoo.org/browse.php)
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. (Info found here:http://cgdb.biocuckoo.org/download.php)
   • 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:
   1. • 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.