CGDB: Circadian Gene DataBase

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 databases 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.

CGDB: Circadian Gene DataBase Slide Deck

CGDB: Circadian Gene DataBase Slide Deck

Electronic Journal

In completing this assignment, Simon and Hayden searched both the Nucleic Acid Research journal and the database itself for the answers to the specified questions.

• For the "General Information" section, two of the four answers came from the database itself. With a little searching, the information was readily available. The other two answers came from the article written about the database found in the Nucleic Acid Research journal.
• For the "Quality of Science" section, the first two answers were found quite quickly on the browse page of the website. The third question took a bit more searching on the site but we were able to find all the necessary information.
• For the "General Utility" section, the links were easy to find in the sources, which came as no surprise because the database was fairly easy to navigate. The convenience of downloading the data left a bit to be desired. This is because they had a great list of sequences which included links in the download page, but when clicked on any of the links... rather than downloading a file to your computer, it seemed to open a new browser page with a TXT file on it, containing the sequence. With all these things considered, we agreed that this database was overall pretty user friendly.

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.
4. Although Simon and Hayden both utilized the sources above, the assignment was completed by Simon and Hayden entirely and not copied from another source.
   Hhinsch (talk) 15:02, 2 October 2017 (PDT)
   Simonwro120 (talk) 15:05, 2 October 2017 (PDT)

References

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

List of Assignments

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Journal Entries

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Shared Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

Assignments

Week 1
Week 2
Week 3
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Week 11
Week 12
Week 14
Week 15

Hayden's Individual Journal Entries

hhinsch Week 1
hhinsch Week 2
hhinsch Week 3
hhinsch Week 4
hhinsch Week 5
hhinsch Week 6
hhinsch Week 7
hhinsch Week 8
hhinsch Week 9
hhinsch Week 10
hhinsch Week 11
hhinsch Week 12
hhinsch Week 14
hhinsch Week 15
Page Desiigner Deliverables Page

Class Journal Entries

Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
Class Journal Week 10
Page Desiigner

Electronic Notebook

Hhinsch Electronic Notebook

Hayden's User Page

Hayden Hinsch