MiRPathDB Week 5

As homework partner, Quinn Lanners and John Lopez worked together to analyze the miRPathDB database by following the template laid out on the week 5 assignment page.

To start this weeks assignment, we selected a database from one of the ones on the Nucleic Acids Research Database Issue Table of Contents 2017. After we had selected a database, and it was approved by Dr. Dahlquist, we began work on the assignment.

To make better use of our time, we decided on Thursday to break up the questions between ourselves. Then we could work separately on our own time to find the answers before coming together to put all of the information into a PowerPoint presentation. We decided that John would handle the questions "General Utility" questions of the database, while Quinn would handle the "Scientific Quality" questions of the database. As for the "General Information", which we figured would be easier to determine, we decided to answer those questions each individually as we looked into our specific part. Since the database research was broken up in this manner, the following section of the electronic journal is comprised of two separate accounts from each of us about how we retrieved the answers to our assigned questions.

• Scientific Quality:

I aimed to answer the following questions regarding our database:

• Scientific quality of the database
  1. 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?
  2. What species are covered in the database?
  3. Is the database content useful? I.e., what biological questions can it be used to answer?
  4. 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?
     • When did the database first go online?
     • How often is the database updated?
     • When was the last update?

In order to answer these questions I read the article covering the miRPathDB from the Nucleic Acids Research and by analyzing the actual miRPathDB website.

• 1. Does the content appear to completely cover its content domain? Answer: Yes this database seems to cover the content domain well. The study of mRNAs appears to be an especially new field, with recent technology advances allowing for much more study on the topic. This database appears to be one of the leading mRNA databases (specifically for Homo sapiens") covering a broad range of information. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)
     • How many records does the database contain? Answer: Contains records for primarily Homo sapiens but also has records on Mus musculus for comparison purposes. There are a total of 2,599 human mRNAs contained in the DB along with 14,773 experimentally validated target genes and 19281 predicted targets genes. (https://mpd.bioinf.uni-sb.de/overview.html)
     • What claims do the database owners make about coverage in the corresponding paper? Answer: They claim to cover a broad range of mRNAs (primarily in Home sapiens) along with target genes, and functional pathways for mRNAs to show how they function. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
  2. What species are covered in the database? Answer: Primarily Homo sapiens with some information on Mus musculus for comparison purposes. (https://mpd.bioinf.uni-sb.de/overview.html)
  3. Is the database content useful? I.e., what biological questions can it be used to answer? Answer: This database can be used to better understand which mRNAs play a role in a variety of human biological pathways. Such understanding may be useful in better understanding a number of pathways and the importance of mRNAs. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
  4. Is the database content timely? Answer: Very much so. With the increasing knowledge on human mRNAs and how they interact with pathways, this DB provides both information on the mRNAs along with a way to analyze this complex information. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
     • Is there a need in the scientific community for such a database at this time? Answer: Yes. They need a way to store and analyze all of the complex information on mRNAs. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
     • Is the content covered by other databases already?: There is a more expansive DB called miRBase, although this database appears to be much harder to navigate and does not have such easy features to analyze how the mRNAs factor into pathways. There is also information in the form of mRNA targets from miRDB, TergetScan, and DianaTools, although these DBs don't have expansive information on the mRNAs. (http://www.mirbase.org), (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target), (http://diana.imis.athena-innovation.gr/DianaTools/index.php), (http://www.targetscan.org/vert_71/), and (http://www.mirdb.org)
     • When did the database first go online? Answer: Can't find this information
     • How often is the database updated? Answer: Can't find this information
     • When was the last update? Answer: Biological categories: 11 Jan 2016. miRNA Targets: 09 Sept 2016. (https://mpd.bioinf.uni-sb.de/documentation.html)

• General Utility:

After we had both individually researched the answers to our questions, we met