Class Journal Week 5
From LMU BioDB 2015
Contents
Jake Woodlee
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- Ethics, Data Visualization, Data Preservation, and Quality Assurance. Ethics has been hammered into me since I was young. By this I mean citation of sources and no plagiarism, so it follows I would be familiar with ethical data usage. I am familiar with data visualization because of my internship last summer. One of Alameda County's mandates from the state is to have various data sets compiled about themselves, as a result they task their IT department to make the data visually appealing to look at and understand. While I wasn't specifically involved with that process, they still taught us about data visualization. I also think I have somewhat of an understanding of Data Preservation and Quality Assurance, because I know a lot of the difficulties database managers face day to day, again because of my exposure to Alameda County's communication infrastructure.
- 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?
- Metadata and Discovery and Acquisition of Data. Metadata is vitally important, as is demonstrated by the article we reviewed. The article provides metadata for their users so users know what to expect within the DDBJ. Without that metadata, the users would have to search through the database themselves just to see if what they are looking for is in the database. I learned this by reviewing the article and realized how confused I would be if I didn't have the data annotated. Discovery and Acquisition of Data sort of falls with metadata. Locating and using the appropriate data repository is based a lot on the quality of metadata available. We reviewed the DDBJ in part on its clarity and without clear comprehensive metadata it is impossible to acquire and discover information.
- Which of these core competencies (if any) do you want to know more about? Why?
- I definitely want to learn more about SQL and database querying just based on pure interest. So I guess that would fall under "Databases and Data Formats". Also, I think it would be useful to learn about Data Conversion and Interoperability just because I noticed that databases commonly work together. As a result converting data to other formats and using a standard format is of utmost importance for inter-database interaction. Furthermore, I would like to know more about how data is curated and re-used in its lifecycle. Our article focused on new additions and data already housed within the DDBJ, I don't remember it talking much about curation.
Jwoodlee (talk) 09:31, 5 October 2015 (PDT)
Veronica Pacheco
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 Data Preservation, Analysis, Visualization, and Ethics. I became familiar with it mainly in the context of research and publication. It is very important for research to be able to maintain, keep and publish reliable research. Its both for the experiment to be doable by other scientists to produce the same or similar results and it must be done in honor meaning that they have to have honest data.
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 think I got a better understanding of Data Management and Organization and Data Format because I understand that organization plays an huge role in terms of efficiency. It is more frustrating for a new person to go through data when its very hard to find or use. Even if the data can be complicated, if it is organized and user-friendly it makes it less frustrating to go through the motions.
Which of these core competencies (if any) do you want to know more about? Why? I would like to learn more about Quality Insurance. I think it is important for any information that goes into a database that it is honest and useable data. That is why I would like to know more about the Quality Insurance and how it plays a role in the greater science community.
Vpachec3 (talk) 09:22, 6 October 2015 (PDT)
Emily Simso
- 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 Discovery and Acquisition of Data, some Data Analysis, Data Visualization, and Ethics. I was primarily exposed to these areas through various classes I've taken in the past. I also learned more about data, and the importance of keeping it organized, at an internship I had over the summer.
- 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 learned about Databases and Data Formats, Data Management and Organization, Data Conversion and Interoperability, Data Curation and Re-use, and Cultures of Practice for the first time through this assignment. I also learned more about Data Analysis, Data Visualization, and Discovery and Acquisition of Data. I think the assignment did a good job of exposing me to a type of database I had never seen before. It also gave me a greater appreciation for the behind-the-scenes work that goes into making a database and the cycle of data. The readings that went along with this week and last week also taught me about the different types of data and languages that exist.
- Which of these core competencies (if any) do you want to know more about? Why?
- I would like to learn more about Quality Assurance and Metadata because I think those both apply to the general population and involve the necessity for data to be accessible. I think that the information comprised in any database should be available for anyone, even if they are not trained in that specific field.
Emilysimso (talk) 22:42, 6 October 2015 (PDT)
Brandon Litvak
- 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 Discovery and Acquisition of Data, Data Visualization, and the Ethics, including citation of data scientific data literacy core competencies prior to taking this class. I came to be familiar with these core competencies through previous work in Biology 111 and 112, which introduced me to the many databases used by biologists to store and retrieve data and to the importance of proper citations (and the importance of building upon the previous work of others). My previous classes also introduced me to the visual language and the various kinds of data visualization that are employed in biology for different kinds of data.
- 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 gained a deeper understanding of Data Conversion and Interoperability,Data Curation and Re-use, and Cultures of Practice. Exploring the database tied to the NAR manuscript deepened my understanding of these core competencies by exposing me to the common file formats used for certain kinds of data, and the shared practices and methods with regards to the sharing and maintenance of data (specifically, database data). Reading the manuscript, additionally, taught me much about the role of certain kinds of data in the scientific community and the importance of adjusting databases in order to complement and support current trends and research in a field.
- Which of these core competencies (if any) do you want to know more about? Why?
- I would like to know more about the Metadata, Quality Assurance, and Data Preservation core competencies, since I feel that these topics are relatively foreign to me, yet are essential for the continued existence of a useful database. It would be interesting to learn more about how data is maintained and checked for errors. “Metadata” seems very important as it makes data more accessible and easily understandable (also helps in the organization of the data); I am interested in learning more about how metadata is used in databases and about its purpose.
Blitvak (talk) 00:14, 7 October 2015 (PDT)
Mary Alverson
- 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 Discovery and Acquisition of Data because I have been taught how to search for data a lot though various courses throughout my education, but most recently in my FFYS class, where we learned how to use the library’s resources, and in Research and Exhibition, where we learn how to find appropriate data sources for our specific disciplines. I was familiar with Quality Assurance also from my Research and Exhibition class. We learned how to guess a data source’s quality by looking at how many times an article has been cited, which shows its validity. We also learned that each discipline has a specific period of time that, once passed, a piece of data is most likely no longer relevant. For disciplines such as Computer Science and Biology, this time period is generally shorter compared to disciplines such as literature. I was also familiar with Ethics, including citation of data by reading the LMU Honor Code. I have seen it a good amount of times because of orientation, and its frequent appearance on class syllabi. The Honor Code is pretty comprehensive when it comes to guidelines surrounding plagiarism and citation.
- 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 gained a deeper understanding of Databases and Data Formats through learning about relational databases in class, and through this exercise applying our learning to understand how our specific and complex database was structured, and how different query options are important tools for the utility of the database. I also gained a deeper understanding of Metadata by seeing how external sources could enhance searches with either references or as a way of identification. Lastly, I gained a deeper understanding of the Cultures of Practice. I did so by reading the review guidelines as well as listening to Dr. Dahlquist’s lecture on the practices of making data public or choosing not to. By having to abide by these guidelines during our review I was able to learn more about the culture of practice specific to biology.
- Which of these core competencies (if any) do you want to know more about? Why?
- I would like to learn more about Data Management and Organization because I don’t think I have a firm grasp on what the lifecycle of data is. I would like to learn more about Data Visualization because so far in class we have started to construct small databases but we haven’t explored many ways to visualize our databases. I would also like to learn more about Data Analysis because so far, in respect to DNA, we have figured out how to analyze DNA enough to find the amino acid strings from codons and base pairs but I would like to analyze those amino acid strings enough to be able to put that data into a context that tells us something about the species that the DNA is from.
--Malverso (talk) 11:38, 7 October 2015 (PDT)
Anu Varshneya
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- Out of the listed core competencies, I became familiar with data preservation, data analysis, data visualization, and ethics including citation of data. I became incredibly familiar with data preservation through understanding the importance of backing up computer onto an external hard drive to prevent loss of data and information. I also learned about the importance of organization of data through experience with keeping folders on my computer/ cloud accounts in order to be able to quickly retrieve files I may be looking for. In Data Structures, I learned about hierarchies of organization that are used in order to keep object oriented code organized. I learned about data analysis explicitly in high school and freshman year when several different types of biological programs were used in order to process data I collected (ex. ANOVA, BLAST, etc.). This understanding was furthered this past summer in SURP when I worked on manually processing microarray data with the Dahlquist Lab. Data visualization is something I am familiar with through experience working with and creating [GRNsight http://dondi.github.io/GRNsight/] with the Dahlquist Lab. Ethics in regards to citation of data is something that has been emphasized since elementary school in a number of different research projects and papers. I also have some understanding of data conversion due through the Dahlquist Lab research projects in regards to formatting files in order to be understood by specific programs, but I am unsure about how much I truly know about this topic.
- 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?
- By doing this exercise, I gained a deeper understanding of databases and data formats, metadata, and data reuse. Through this exercise, I was able to explore a database and learn more about how to accurately pinpoint information that I wanted to locate with specific search queries. I also was exposed to a couple different ways that the database that I explored presented the information on its page including on page text and downloadable files. I was also more informed about metadata. Though in class we annotated a small sequence of nucleotides, this database had extensive guidelines regarding how to properly annotate any submissions. Finally, with this exercise I was exposed to an example of data reuse as some databases work via submissions from other sources.
- Which of these core competencies (if any) do you want to know more about? Why?
- I want to learn more about the cultures of practice in regards to data in databases as this exercise only exposed me to one database, so I am still unsure of overarching standards that all databases should comply with. Furthermore, I would like to learn more about data management and the lifecycle of data because I think that would be helpful in organizing large datasets in a database.
-- Anuvarsh (talk) 15:41, 7 October 2015 (PDT)
Kevin Wyllie
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- I'd like to think that I was familiar with "ethics, including citation of data," as this applies to not only databases, but scientific data as a whole. I'm familiar with the idea of using concise formats of citation so that someone reading my work can trace back to the original source. This is something I've learned during my time as a biochemistry major. Another more general concept I've picked up as an undergraduate is "discovery and acquisition of data." One specific example of this is my chemistry seminar class, in which we had to do quite a bit of searching among scientific literature to find studies that would be appropriate for a formal presentation. "Data conversion and interoperability" is something I vaguely grasped during my time in the HHMI Phage Lab course. The first thing that comes to mind is the FASTA format of nucleotide sequences, which can be entered into various different bioinformatic software.
- 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 became familiar with "data curation and re-use" when working on the essay portion of this assignment, due to the prompt-question asking about that process. Wrestling with "data management and organization" in this assignment was a bit tough, because in my group's case, there were many subsets of data, and different function which took data from different subsets. So that's another concept I became familiar with. I feel that I may have scratched the surface of "databases and data formats" as well, now having some familiarity with databases which recognize relationships between different groups of data. (Sorry, it was difficult to give specific answers without breaking confidentiality!)
- Which of these core competencies (if any) do you want to know more about? Why?
- I don't know much about "data preservation," unless common hardware knowledge (ex: thumb drives) counts. I know next to nothing about things like servers, which I think is relevant both in and out of the biological databases/system biology field. "Cultures of practice" sounds particularly interesting because it could potentially vary within different fields of database-involved sciences, and I wonder to what extent database culture it overlaps with general computer science culture (which interests me after the Ford reading).
Kwyllie (talk) 23:15, 7 October 2015 (PDT)
Mahrad Saeedi
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- I am familiar with certain core competencies from the given list before taking this class. Specifically, I am familiar with data curation, analysis, visualization, and ethics, including citation of the data. I have been exposed to these core competencies in working with a friend of mine who is a finance major involved in creating applications for android and apple. I assisted him in curating content for a new social networking app that he was working on. In addition to curating content, I have had experience analyzing and presenting certain data. As a biologist, the research projects I have worked on require skills with handling, analyzing, and being able to portray the data visually. Furthermore, research experience has provided me with knowledge regarding the ethics of collecting and citing data.
- 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?
- With this exercise, I was able to gain insight on many of the core competencies I had been unfamiliar with. Specifically in the areas of: databases and data formats, discovery and acquisition of data, data management and organization, metadata, and cultures of practice. Through exploring the NCBI database and over-viewing their comprehensive manuscript, I have come to understand the purpose of a database and how different types of data are managed and organized differently. The manuscript did a good job of orienting me to the cultures of practice involved with curating and storing data.
- Which of these core competencies (if any) do you want to know more about? Why?
- I want to know more about data conversion and interoperability and quality assurance. These are the core competencies I have the least experience with and am curious of how each can be accomplished when it comes to such a large database. I am interested in further understanding how data can be converted and still serve the same purpose.
Msaeedi23 (talk) 23:19, 7 October 2015 (PDT)
Trixie Roque
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- I’ve been familiar with Discovery and Acquisition of Data, Data Analysis, Data Visualization, Ethics, including citation of data before taking this class. Because there is a need for internet usage for research purposes in academia (starting from when I was in high school, I believe), I’ve learned/been taught how to query for certain journal articles, analyze and visualize the data they provide, and credit their owner/author. Since the internet is scattered with all kinds of information, learning to use proper databases with reputable information was necessary; my high school classes wouldn’t allow citation of just wikipedia pages. Analyzing the information and presenting them in a neat format was also necessary for my classes since high school; since the information was never mine, I also had to remember the sources where I got them from.
- 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?
- Aside from the ones I am already familiar with (see question 1 for those core competencies), from doing the assignment, I also gained a better understanding of Databases and Data Formats. Even though I’ve used databases frequently when creating a research report, I never really tried to understand the types and formats for the files in them. I had to apply the ones I’m already familiar with in making the review and the presentation since I still had to research some terms from databases, analyze the results, make them into visually appealing images, and credit the owners. However, I’ve also gained a better understanding of databases querying since we actually had to do a demo/take screenshots of the databases themselves in order to properly and clearly show our peers how the databases we are assigned work.
- Which of these core competencies (if any) do you want to know more about? Why?
- Data curation/cultures of practice (both contain an element of curation) has piqued my interest since the first time I encountered the term “curation” when dong the manuscript so I would like to know more about it. In making the review, we touched upon what it means, but I would like to know exactly the process the database undergoes when someone curates it (both electronically and manually). Since the article we reviewed is one of the biggest databases for containing important scientific research, I’m curious as to how the staff manages the large sets of data (not to mention that they update the database regularly, which is an amazing feat in itself).
--- Troque (talk) 23:47, 7 October 2015 (PDT)
Brandon Klein
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- Before taking this class, I would consider myself to have been familiar with the following listed core competencies: discovery and acquisition of data; databases and data formats; data analysis; data visualization; and ethics. In the past academic year, I completed coursework involving cladistics that used the Basic Local Alignment Search Tool (BLAST) offered by the National Center for Biotechnology Information that familiarized me with the discovery and acquisition of data as well as databases and data formats. Over summer during the advancement of my biomathematics research project, I did further work with a database of biological data that advanced my understanding of data analysis and visualization. Finally, I feel as though my coursework thus far has imparted a good understanding of ethics to me.
- 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?
- During the execution of this week's project, I gained a deeper understanding of several of the core competencies. In working with the assigned database, I greatly advanced my existing knowledge of databases and data formats as well as the discovery and acquisition of data. In addition to this, I learned about new core competencies while exploring the database including data management and organization; data curation and re-use; and data preservation. During my investigations of the database, I found myself reading in detail about the manner in which the data was curated and maintained in the database over a long period of time. I thought the details I read regarding the lifecycle of data were particularly interesting, as we tend to consider data as relatively static.
- Which of these core competencies (if any) do you want to know more about? Why?
- I would like to learn more about all of the core competencies that I am not already familiar with to build up my foundational knowledge for work with biological databases. Particularly though, I am interested in acquiring specific knowledge in a few of these topics. One of these areas is metadata. I have limited experience with metadata but am very interested in the way it is handled as well as the implications of metadata studies. In addition to this, I feel as though I could always benefit from brushing up my understanding of modern data analysis and visualization techniques, as these are crucial to understanding the concepts conveyed by a database (or a great deal of research in general). Finally, I am interested in how quality assurance functions. I feel as though this core competency is one that I take for granted, but that must be very important in the creation of databases. In addition to this, I find it interesting to think about what kinds of data may be removed form a database and whether or not this could accidentally weed out important information if the process is automated.
Lena Olufson
- Which of these core competencies (if any) were you familiar with "before" taking this class? How did you become familiar with them?
- I think that I was familiar with the core competencies of Cultures and Practice and Ethics, including citation of data before taking this class. Throughout my schooling I have been taught that citation of your data and work is the most important thing you should check before submitting or turning any paper or project in. Citation is very significant in the real world as people can get fined and discredited if it is determined that their work is not their own. I think that the rules of citation for a paper are the same as for a citation of data in the sense that you must give the source and where the data came from otherwise it is considered plagiarism. I think that ethics is also a key part of the citation and sharing of data because sometimes people can be protective of their individual genome sequences and so they maybe do not want their information shared with the public. This ties into the cultures of practice as the values and norms of separate persons should be respected when using data that is not your own.
- 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 learned more about a lot of the core competencies by doing this exercise because I have never really explored or interacted in depth with a database before online. A couple of the main competencies I thought I got a better grasp of are Databases and Data Formats, Metadata, and Data Management and Organization. For Databases and Data Formats, I think that just exploring the home page of the database was very helpful to me as I was able to search for various things using the search tool, as well as navigate through other links that were provided by the database. The formatting of the data was also a new learning experience for me and I was able to see how it ties into the discipline and the layout of the database as a whole. Metadata was also a big aspect of the database I analyzed because it was used to limit the amount of time and effort users had to expend to search the database. The Metadata was very helpful in clarifying the data presented and without it I think that I would have been very lost trying to locate certain things within the database. Data Management and Organization became more apparent to me during this assignment because I was able to see how the database was designed in order to be user-friendly, aesthetically pleasing, and provide the necessary information. By exploring the database, I saw how important the management and organization of data is in order to be an effective and appealing database to all users.
- Which of these core competencies (if any) do you want to learn more about? Why?
- I would like to know more about the Data Conversion and Interoperability as well as the Data Analysis and Data Visualization competencies. I do not know anything currently about converting data and I am unsure of what the word interoperability means, so I think that I would further my knowledge greatly of databases if I learned more about this subject and how it can benefit me when developing my own database in the future. I also think that Data Analysis and Data Visualization would be very useful to me because I would be able to feel more comfortable manipulating and working with a particular set of data. I am not confident or comfortable with editing and using tools to analyze the data right now, but I would like to gain more experience and practice working with these competencies so that I can learn their significances and benefits.
Lenaolufson (talk) 11:14, 8 October 2015 (PDT)
Kristin Zebrowski
- 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 Data Preservation, Analysis, and Visualization as well as Ethics. In many of my biology courses we have had to use scientific articles and either cite them appropriately or use them in presentations. I don't think I have had a single biology class where I haven't had to analyze different data sources and attempt to understand and interpret them, which gave me exposure to Discovery and Acquisition of Data. Furthermore, I've had a lot of exposure to ethics in my entire academic career at LMU and in high school. I have always been taught to give credit to those where credit is due.
- 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 definitely have gained more insight into the Ethics core competency through this exercise and even through this course even though I already felt I had a thorough understanding of what it means. I have also gained significant insight in the areas of Databases and Data Formats as well as Data Conversion and Interoperability--the only previous experience I had were with BLAST in Gen Bio lab. The experience taught me that not only is it useful to understand how to search relational databases and be familiar with them but it makes it much easier to find tools and resources if the formats are standardized. Furthermore, this assignment taught me about Quality Assurance as we checked over our groups' given databases and looked for errors/gave critiques relating to other areas of discipline such as Data Preservation. This is the first experience I've had with official peer reviewing in an academic journal setting and I feel like it really showed me how meticulous, but also how essential, the process is.
- Which of these core competencies (if any) do you want to know more about? Why?
- I want to know more about Metadata. I really don't know very much about metadata at this point, so I would like to be able to annotate my own data so that it can be used by other users. I would also like to learn more about Cultures of Practice as I haven't really curated my own data and the field of bioinformatics is still very new to me. I would like to become more competent in these areas because I think it will ultimately help me to understand the field better and be more productive with my contributions to it through this course.
Kzebrows (talk) 16:42, 8 October 2015 (PDT)
Josh Kuroda
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- Because of the various computer science classes I have taken so far, I was a little familiar with the data management and organization competency, as well as the data visualization competency. I feel that my Data Structures class in particular helped me to further my understanding of these concepts, and I could make connections between what I had learned to this assignment.
- 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 two competencies about which I learned the most were data analysis and quality assurance. I think that analyzing the database assigned to my group really forced me to learn about how a consistent and clear analysis of data is an important aspect to any medium used for research. In addition, I found that making sure each and every result is legitimate and of a certain quality is paramount when aiming for a good user interface and experience.
- Which of these core competencies (if any) do you want to know more about? Why?
- I think I would like to learn more about the cultures of practice so that I can be more familiar with the overall data sharing environment and ecosystem. From what I have learned, it seems like a very open and forward-thinking community, and it would be great to learn more about the intricacies of database management and collection.
Jkuroda (talk) 16:50, 8 October 2015 (PDT)
Nicole Anguiano
Note: My assignment was completed on time, as can be viewed in the history. However, it appears it was deleted sometime after I posted it.
- 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 databases and data form, discovery and acquisition of data, data management and organization, quality assurance, data analysis, data visualization, and ethics. I knew about most of these from my study of databases and the research projects I've done in the past.
- 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 personally don't feel that I gained a deeper understanding of any of the core competencies by doing this exercise. If I had to choose one, I learned a bit more about data curation. It was interesting to see that the database was evolving and removing out-of-date databases (or so was assumed, as there was no available changelog).
- Which of these core competencies (if any) do you want to know more about? Why?
- I want to learn more about cultures of practice. I know primarily about how data is analyzed and displayed from the perspective of the computer scientist. However, I would be interested to see how data is handled by the users, and the norms established by those in bioinformatics who deal routinely with data.
