Class Journal Week 5

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

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

Laurmagee (talk) 23:45, 26 September 2013 (PDT)

Kevin Meilak

Database: Spliceosome Database

Database Website: Spliceosome Database

Kevin Meilak: Response to Reflect Questions

1. I was familiar with Discovery and Acquisition of Data, Cultures of Practice, Data Preservation, Data Analysis, and Ethics, including citation of data. I became familiar with these aspects through research papers for classes which required familiarity with the relevant data for the field (typically biology, but also liberal arts such as theology and philosophy), and by doing research through the Summer Undergraduate Research Program (SURP) this past summer at LMU.
2. By doing this exercise, I now feel that I have a better understanding of Databases and Data Formats. Finding information about and acquiring information from a database I had never interacted before and whose contents were (and remain) foreign to me required that I understand data in different formats (in this case a spreadsheet as opposed to text or graphical depiction). Furthermore, more practice interacting with a database allowed me to grow more comfortable interacting with databases.
3. I would like to know more about metadata because I have had little if any experience with it despite it being a powerful analytic tool.

Kmeilak (talk) 18:17, 29 September 2013 (PDT)

Kevin McGee, Viktoria Kuehn

Database: Ensembl

Database Website: http://uswest.ensembl.org/index.html