RNAct Week 5
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Contents
Links
General Information of the Database
- What is the name of the database? (http://rnact.crg.eu)
- 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?]) (http://rnact.crg.eu)
- The biological information that it contains deals with interactions 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?]) (http://rnact.crg.eu)
- What individual or organization maintains the database? (http://rnact.crg.eu)
- public versus private
- Private
- large national or multinational entity or small lab group
- A small lab group named Tartaglia Lab, that is helped by Center of Genomic Regulations (CRG).
- 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?
- The database appears to completely cover its content domain because it obtains proteome data from UniProt and transcriptome data 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 as explained in the materials and methods section.
- What species are covered in the database? (If it is a very long list, summarize.)
- On the home page below the search bar Homo sapiens, Mus musculus, and Saccharomyces cerevisiae are listed as the current species available and C. elegans, Drosophila, and Arabidopsis are intended to be added.
- Is the database content useful? I.e., what biological questions can it be used to answer?
- In the description section 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. The information gained from predicting the RNA-protein interactions can be used, along with RNA-RNA and protein-protein interactions to create a map of all molecular interactions in an organism to understand it completely physiologically. Other RNA-protein interaction databases do exist, including PRD, PRIDB, etc.
- How current is the database?
- The database first went online in 2018. The paper states in the materials and methods section that the yeast non-coding transcripts were from Ensemble 92 release in April of 2018.
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. It only involves predictions and experimental data from the interactions. Unlike other databases, this solely focus on protein-RNA interactions.
- Is it convenient to download the data?
- The data is convenient to download in .zip format from the download page.
- 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 (example). 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 disambiguous list to specify the proteins and RNAs. After selecting the desired protein or RNA I was given another list of the RNA sequences that interact with the protein, along with a prediction score and the associated fold change.
- Access: Is there a license agreement or any restrictions on access to the database?
- The license agreement states that the proper credit must be given to the creators and provide a link to the licence, also the database may not be used in for commercial purposes, and finally if the database is altered or built upon the proper credit must be given to the creators.
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 professional database because it consists of several experimental data from a variety of databases. Therefore, it consists of a great deal of information. However, there is always room for improvement.
Database Powerpoint Presentation
File:Avila Crespin BioDB Presentation1.zip
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
- Dr. Dahlquist helped with presentation guidelines.
- "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)
Mavila9 (talk) 21:31, 30 September 2019 (PDT)
References
Lang, B., Armaos, A., & Tartaglia, G. (2017, November). RNAct. Retrieved from https://rnact.crg.eu/.
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
