Difference between revisions of "RNAct Week 5"

Revision as of 21:12, 29 September 2019

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 million 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
What individual or organization maintains the database?
- public versus private
  - Private
- large national or multinational entity or small lab group
  - Small lab group
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.

Does the content appear to completely cover its content domain?
- How many records does the database contain?
- What claims do the database owners make about coverage in the corresponding paper?
What species are covered in the database? (If it is a very long list, summarize.)
Is the database content useful? I.e., what biological questions can it be used to answer?
Is the database content timely?
- Is there a need in the scientific community for such a database at this time?
- Is the content covered by other databases already?
How current is the database?
- When did the database first go online?
- How often is the database updated?
- When was the last update?

Are there links to other databases? Which ones?
- Yes, there are other databases that have been linked in this one. The two that have been mentioned are NCBI and ENCODE.
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)?
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?

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.

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)

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

@@ Line 54: / Line 54: @@
 == 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 [https://rnact.crg.eu/about About] page, the creators discuss about the future of their page. Therefore, it is a working progress.
 == Database Powerpoint Presentation ==