Difference between revisions of "RNAct Week 5"
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== General Utility of the Database to the Scientific Community == | == General Utility of the Database to the Scientific Community == | ||
Revision as of 12:03, 30 September 2019
Contents
Links
General Information of the Database
- What is the name of the database? (link to the home page)
- The name of the database is RNAct
- What type (or types) of database is it?
- What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
- The biological information that it contains deals with structure of proteins and the RNAs itself. It involves predictions/interactions with over 5 billion genomes of humans, mouse, and yeast.
- What type of data source does it have?
- primary versus secondary ("meta")?
- It is a secondary source.
- curated versus non-curated?
- Curated
- if curated, is it electronic versus human curation?
- Electronically curated
- primary versus secondary ("meta")?
- What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
- What individual or organization maintains the database?
- public versus private
- Private
- large national or multinational entity or small lab group
- Small lab group
- public versus private
- What is their funding source(s)?
- Their funding source comes from Horizon 2020. It is an EU research and innovation program that has funds lasting from 2014-2020.
Scientific Quality of the Database
- Does the content appear to completely cover its content domain?
- Yes, the database obtains proteomes from UniProt and transcriptomes from GENCODE and Ensembl, all of which are reliable and comprehensive sources. The database contains 20778 human proteins, 22080 mouse proteins, and 5963 yeast proteins from Uniprot, all used to predict a total of 5.87 billion RNA-protein interactions in the respective species.
- What species are covered in the database? (If it is a very long list, summarize.)
- Homo sapiens, mus musculus, and saccharomyces cerevisiae.
- Is the database content useful? I.e., what biological questions can it be used to answer?
- The authors of the article say that they intend their database to be used for studying gene regulatory events and networks at the post-transcriptional level.
- Is the database content timely?
- There is a need for this database in the scientific community because it helps predict RNA-protein interactions in humans, yeast, and mice which are all widely studied organisms. Mice and yeast specifically are model organisms. The interactions between proteins and RNA are necessary to understand in many biological research investigations as they work together in making up an organisms characteristics. Other RNA-protein interaction databases do exist, including RAID, NPInter, PRD, etc.
- How current is the database?
- When did the database first go online?
- How often is the database updated?
- When was the last update?
- marcus
- marcus
- marcus
- marcus
- marcus
- marcus
General Utility of the Database to the Scientific Community
- Are there links to other databases? Which ones?
- Is it convenient to browse the data?
- It is convenient to browse the data if the user has a specific RNA/protein and knows what they are seeking for. If it contains anything but a protein, it tends to get confusing. Overall, the database doesn't contain as much information as the user will hope. This can be the case when searching a name, clicking through links, and noticing it is "somewhat" on the same page.
- Is it convenient to download the data?
- In what file formats are the data provided?
- What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
- Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
- In what file formats are the data provided?
- Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
- Is the website well-organized?
- Does it have a help section or tutorial?
- Are the search options sensible?
- Run a sample query. Do the results make sense?
- Access: Is there a license agreement or any restrictions on access to the database?
Summary Judgment
- Would you direct a colleague unfamiliar with the field to use it?
- No, this would not be directed to a colleague that is unfamiliar with the field. As mentioned before, this database is for those who understand what they are looking for. Since it is specifically about proteins and the interactions between different databases, it can get very confusing.
- Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, and seems amateur.
- This is a "hobby" database because it was done by a small group of interviews who are still testing things and trying to see how to improve it. In their About page, the creators discuss about the future of their page. Therefore, it is a working progress.
Database Powerpoint Presentation
Acknowledgements
- This week's journal was completed by Marcus Avila and Iliana Crespin
- Homework partners messaged and consulted on how much contribution each person was going to put in this assignment
- "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."Icrespin (talk) 19:48, 29 September 2019 (PDT)
References
Week 5 Assignment page is: LMU BioDB 2019. (2019). Week 5. Retrieved September 29, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5
