RNAct Week 5
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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?
- The database first went online in 2018. The database is updated monthly because an algorithm is used to take information from the source databases to predict the RNA-protein interactions.
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?
- Yes downloading the data is convenient.
- In what file formats are the data provided?
- The data is downloaded in .zip format.
- Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
- The website's home page is very clear and even includes some example search terms to help the user understand what can be searched. After entering a search term the user is given a list of proteins and RNAs that are disambiguous. The user can then look through a list of related known RBGs. The search results page also gives a prediction score and rating to inform the reader about the accuracy of the prediction. The database does not include a help section or tutorial, but provides use information in the About section. The search options are sensible and the examples under the home page search bar help guide the user in properly searching a protein or RNA sequence.
- Run a sample query. Do the results make sense?
- I searched "Gemin5" and was given a list of disambiguous proteins and RNAs. After selecting the desired protein or RNA I was given another list of proteins and their corresponding RNA sequences along with a prediction score and the associated fold change.
- 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
