Class Journal Week 5

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Class Journal Week Five

Contents

Tauras, Lena, and Miles

Database: TFClass

Database Webiste: TFClass

Tauras' Reflection

Note: the subsections are not clearly defined. Each Competency was placed in the category(ies) it most directly applied to. Some appeared in more than one category and others were condensed into the major area.

Competencies I was familiar with

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

  • Databases and Data Formats: I had worked previously with NCBI-Blast and a few other databases so I was generally familiar with how to make a search query and knew how to download/use some file formats. As we didn't download files and work with them in another program, I feel like I did not learn more about data types or formats.
  • Data Conversion and Interoperability: Working with DNA sequences and identifications in other research projects, I had some idea of the issues of different names used in different databases. This exercise demonstrated this a more systematic problem than I had thought, but one that is negated in part by databases such as UniProt linking to multiple other formats. This de facto provides a hub to search for data that appears in different formats or under different names.
  • Metadata: I was already familiar with metadata from reading review papers and the idea of metanalysis in research and behavioral genetics. This exercise clarified some of the ways databases present data from other sources but did not do much to increase my understanding.
  • Culture and Ethics: I already had a good understanding of the ethics and culture of using databases just from common sense and working on research projects. For the most part, it seems like everyone is willing to share data if cited properly, provided the other party is not using the data in a for-profit enterprise.

Competencies I learned more about

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?

  • Discovery and Acquisition of Data: I learned about how different databases collected data and means of curation during lectures. I had never really thought about the question before, but when it was brought up it made a lot of sense and I was able to find out how different groups collect their information.
  • Data Management and Organization: Before this exercise, I knew a bit about database management in a vague theoretical sense. However, doing specific research on TFClass and listening to other presentations helped me understand how different groups deal with the problems of data management and updating.
  • Quality Assurance: Like data discovery, this was something I had never really thought about working with databases. However, during lecture it was brought up as a question and I started to think about how difficult it must be to make sure data is reliable and also update as additional data becomes available.
  • Data Curation and Reuse: I had known data curation must be a problem for databases, but I hadn't really thought about how they go through it. During this class, I learned about the processes used while researching for our database project and during the lecture by Dondi.
  • Data Visualization: Like other features in this category, I had never really thought about the options a programmer has to make in formatting the interface for their database. Looking at databases and using them, I learned a lot about how different types (like lists, separate pages, etc) influenced the viewing experience and the ease to find data.

Competencies I want to know more about

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

  • Discovery and Acquisition of Data: This is still a relatively new idea to me and I would like to know a lot more about how it works. In particular, how do you account for and attempt to cover the vast amount of current molecular data being produced and synthesize it in some meaningful way without compromising quality?
  • Quality Assurance: QA is another field I would like to learn more about. I'm less worried about independent labs and small databases, but how do the large ones like GeneDB and Uniprot stay updated, avoid proliferating faulty information, and react to new advances? This question seems important as it questions the reliability of all types of data
  • Data Visualization: I would still like to learn more about how they actually design the database. I just think this would be a useful skill to have if I ever want to design either a lab or personal webpage.
  • Data Preservation: I still feel like I don't know much at all about how data is actually preserved or how servers work. I don't know why I would ever need to know this, but I think it would be interesting to know about. (This is one of the field's where I still don't know what I don't know.)


Taur.vil (talk) 22:10, 3 October 2013 (PDT)

Hilda and Mitchell

Database: Protogen

Link to Website: [Protogen]
Link to Presentation: File:Protegen.pdf
Link to Wiki Page: Protegen
  1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?

The twelfth core competency would be the most familiar concept that I can relate to since as a student I've had to learn about citing data in my essays or in projects.

  1. 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?

The first, second, seventh, and ninth competencies are ones that I have gained a greater understanding for since I was able to see how databases have links to other databases to provide more information that they may lack in providing. Each database has its own specialty, so knowing what you want to research can help in pin-pointing the appropriate database. I also have a deeper understanding in data curation whether it be manually or electronically and in-house or community manual curation since I had to figure out what methods of curation the database Protegen used. The ninth competency, in my opinion, goes hand-in-hand with the seventh competency in terms of data preservation which includes curation, updates, and database networking and relevancy.

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

I would like to learn more about the eleventh competency since I am a big visual learner, so learning how to use visualization tools would be interesting to learn about and use frequently for future projects.

HDelgadi (talk) 20:54, 3 October 2013 (PDT)

Alina, Stephen

Database: OrganelleDB
Website: [1]

Reflection (Alina)

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

I was familiar with the ethics competencies, having taken science and engineering ethics one semester, where there was a huge focus. It is a topic highly stressed in most scientific settings.

  • 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?

'Databases and Data Formats' and 'Discovery and Acquisition of Data' were greatly improved, as we were forced to navigate different databases and find answers to questions about them. Looking at different kinds of databases gave me a better knowledge of what kind of information storage is actually available.

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

'Quality Assurance' seems like something I would interested in learning more about, specifically being able to recognize flaws in data sets, etc.

Ajvree (talk) 21:39, 30 September 2013 (PDT)

Reflection (Stephen)

  • Prior to this class, I was already familiar with Databases and Data Formats, Discovery and Acquisition of Data, Data Analysis, Data Visualization, and Ethics, including citation of data. Most of these skills were introduced to me when I took freshman biology lab. These skills were further developed when I started doing independent research and was presenting at conferences.
  • This exercise helped enforce the aforementioned competencies. In addition, I am more well attuned to Data Curation and Re-use and Cultures of Practice after this exercise. Doing research on how the research is synthesized and made available was a very different experience for me and helped introduce me to these core concepts.
  • Quality Assurance and Metadata are two competencies I feel I should improve upon. Both competencies are a bit confusing to me, but I believe they would be very helpful with the independent research I am doing. At the very least, I'll be continously be dealing with biological databases for a while.

Slouie (talk) 02:51, 3 October 2013 (PDT)

Katrina Sherbina and Gabriel Leis

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

Gabriel Leis: Response to Reflect Questions

  1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
    Prior to this course I became familiar with scientific data literacy core competencies numbers 1, 2, and 12. I became familiar with these competencies through academic and scientific research and through Biochemistry lab.
  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?
    3, 6, 7, 8, 9, 10 This exercise developed my understanding of core competencies 3, 6, 7, 8, 9, and 10. The article regarding UniProt contained a fair amount of information regarding these core competencies. Core competencies 8, 9, and 10 in particular were developed through information in the UniProt article. The group presentations were also very informative. Both the processes of preparing a presentation and listening to the presentations were informative. The presentations were particularly informative of core competencies 6 and 7.
  3. Which of these core competencies (if any) do you want to know more about? Why?
    Data visualization and data conversion are two topics I would like to know more about. I think data visualization is an excellent way to learn and remember data in a short period of time. I have almost no knowledge of data conversion or data formats and therefore think it would be wise to learn about these competencies

Gleis (talk) 22:21, 3 October 2013 (PDT)

Katrina Sherbina: Response to Reflect Questions

  1. I was familiar with the "Discovery and Acquisition of Data", "Data Analysis", "Data Visualization" and "Ethics, including citation of data" core competencies before taking this class. The first three competencies I have practiced frequently through research I have conducted both on campus with Dr. Dahlquist and Dr. Fitzpatrick and with a cancer biology lab in Boston this past summer. I became familiar with the fourth competency mentioned in previous classes I have taken with Dr. Dahlquist.
  2. I gained a better understanding of the "Metadata" core competancy in that I learned what metadata is and how to make sense of it by exploring the UniProt database through this week's individual activity. Through exploring the features of the PrePPI database as well as the UniProt database this week, I gained a better understanding in the "Databases and Data Formats" core competency. In addition, I gained a greater exposure to the "Data Curation and Re-use" as well as the "Cultures of Practice" competencies in determining how the PrePPI database is curated and who is allowed to use the information in the database and for what purposes.
  3. During the remainder of the class, I would like to learn more about how data is actually stored in databases as well as what methods are used to detect data that has been corrupted (i.e. "Data Preservation" and "Quality Assurance" core competencies).

Ksherbina (talk) 22:40, 3 October 2013 (PDT)

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

Lauren Magee: Reflection Questions

  1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
    • I was pretty familiar with all of these competencies before taking this class, because I was involved with a freshman research lab dedicated to building up phage databases. In the lab, we sequenced the genome of a phage that had been isolated, by one of our peers, from a soil sample on campus. We then inserted this information into the phage database and related it to others that may have already been found and sequenced.
  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 thought more about the “Ethics” competency during this exercise, because I had never thought to look at who contributes to these databases and who modifies them. Databases always seem to be so public that I assume no one owns the right to them, but from answering the questions above, I realized all that goes into the management of the database.
  3. Which of these core competencies (if any) do you want to know more about? Why?
    • I would love to learn more about “Data Visualization”, because I am very drawn to the creative arts. I noticed the way each database expresses their data, sets the tone for my personal understanding of what they are offering to the reader. If the visuals are fun, clear, and concise, I can pick out information with ease. If not, however, I become easily frustrated with the database and move onto another that might be organized more effisciently.

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

Viktoria Kuehn

  1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
    • I was most familiar with numbers 11 and 12. I am a very visual learner so I appreciate the use of various ways of displaying data so that is why I am familiar with using data visualization through my biology courses. I have taken a bioethics philosophy course where we talked a lot about intellectual property, which is why I am familiar with 12.
  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?
    • Through this project I have learned the importance of Data Conversion and Interoperability because it is so much easier to work with large amounts of data if they are easier to categorize and to incorporate in various databases. I have also learned about the importance of data curation, and how much constant upkeep is necessary to run a database with up to date information.
  3. Which of these core competencies (if any) do you want to know more about? Why?
    • I would like to know more about Quality Assurance because it seems like a useful skill to have; to be able to tell when data has been tampered with.

Vkuehn (talk) 19:25, 2 October 2013 (PDT) Database Website: http://uswest.ensembl.org/index.html

Kevin McGee Responses

  1. I was familiar with discovery and acquisition of data before this assignment. I, like the rest of the world, use google and many other types of databases (like facebook) to look up information every day.
  2. I learned about curation and reuse of data. Ensembl has a system of pipelines that allow it to automatically curate data from other sources.
  3. I would like to learn more about Data preservation, analysis and visualization. All three of these competencies seem essential to me when looking at how to interpret scientific data.

Kevinmcgee (talk) 19:32, 2 October 2013 (PDT)

Mitchell Petredis

  1. I was familiar with Data Management and Organization, Cultures of Practice, and Data Preservation core competencies prior to taking this class via my various jobs at Information Technology Services (ITS), where the primary objective was to utilize software such as DeepFreeze to prevent excessive files from accumulating on publicly available computer hard drives and to install core updates to those computers when needed or on a schedule
  2. I gained a better appreciation of the importance of Quality Assurance and Data Curation by doing this exercise by realizing that potentially many people utilize these databases constantly for research purposes; being able to provide the latest, verified information on a regular basis is vital to the integrity of the scientific community.
  3. I'd like to learn more about Data Analysis so that I can fully understand the information behind all the results of a query and how to use them properly.

Mpetredi (talk) 15:57, 2 October 2013 (PDT)Mitchell Petredis

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