Difference between revisions of "Class Journal Week 5"

Revision as of 02:45, 27 September 2013

Class Journal Week Five

Tauras, Lena, and Miles

Database: TFClass

Database Webiste: TFClass

Hilda and Mitchell

Database: Protogen

Link: [Protogen]

Information

Protegen

1. [Protegen]
2. Protegen contains curated information about protective antigens that are able to stimulate the production of antibodies and/or cell mediated immunity against specific pathogens. [Introduction]
3. This database has allowed for the "storage, annotation, comparison, and analysis of 854 protective antigens for 200 pathogens, including more than 50 protective antigens for cancer and allergy (Yang, Sayers, Xiang, He 2010). [Introduction] [Statistics]
4. Protective antigens and pathogens that include antibodies, bacteria, viruses, and parasites. [Introduction]
5. Protective antigens, bacteria, viruses, parasites, fungi
6. Biological Questions
   • What are protective antigens ?
   • Importance of identification of protective antigens
   • Protective Antigens as biological markers

#Computerized and manual in-house and community curated [[Semi-automatic annotation of protective antigens]

1. University of Michigan Medical School, Ann, Arbor, MI.
   • Webmaster: Zuoshuang Xiang
2. Funding is provided by the National Institutes of Health-National Institute of Allergy and Infectious Diseases grant (R01AI81062) [Funding]
3. No. [Disclaimer]
4. Database is SUPPOSED to update every quarter
   • Most recent update was on November 11, 2011 [Updates]
5. Yes
   • [PubMed]
   • [Protein Data Bank]
6. Yes [Data Download] [Data Transfer and Download]
   • FASTA
   • HTML
   • EXCEL
   • OWL formats
7. User-Friendliness
   • Yes (look for yourself: [Protegen])
   • Yes [Help]
   • Yes. Provides links to relevant information pertaining to my query (RB51)

Alina, Stephen

Database: OrganelleDB
Website: OrganelleDB

Katrina Sherbina and Gabriel Leis

• Database: PrePPI
• To use the database, go to the following link: PrePPI

Gabriel Leis: Response to Reflect Questions

Katrina Sherbina: Response to Reflect Questions

Lena Hunt

1.) Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?

• I think I was fairly familiar with 1 (Databases and Data Formats) because I have used a few databases in other classes and understood how to search them, 11 (Data Visualization) because my cell function class used data visualization a lot to show how proteins work, and 12 (Ethics) because, as a college student, we are constantly reminded to cite our sources and not to steal information.

2.)Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?

• I am not sure that I have gained a significantly greater understanding of any of these. The lecture materials helped, but databases are still pretty mysterious. I maybe understand 2 (Discovery and Acquisition of Data) better because of all the various databases I looked at in the Uniprot exercise.

3.)Which of these core competencies (if any) do you want to know more about? Why?

• I would like to know more about 4 (Data Conversion and Interoperability) because I think it is important when working with data to be able to use that data in various format. Of course, I am sure all the items in the list are useful to know more about as well.

Lena (talk) 17:37, 26 September 2013 (PDT)

Lauren Magee & Dillon Williams

• Database: GeneDB