MiRPathDB Week 5

Lab Notebook

Planning the Project

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.

Questions

• General Information: (answered on October 1st by John)

1. The name of the database is miRPathDB Source: (https://mpd.bioinf.uni-sb.de/overview.html)
2. Two answers:
   1. This database contains mainly miRNA molecules and the different pathways you can find said molecule in. Source: (https://mpd.bioinf.uni-sb.de/about.html)
   2. Since the data for the database is collected through several previously-established databases, it is considered a secondary database. It is curated constructed using computer programs, electronically. We know it was made using in-house staff because all of the researchers’ names are listed. Source: (https://mpd.bioinf.uni-sb.de/about.html)
3. It would appear that the Center for Bioinformatics at Saarland University maintains the database. They are a large, public research university. Sources: (http://www.uni-saarland.de/en/info/university/about.html), (https://mpd.bioinf.uni-sb.de/about.html)
4. Only the funding for keeping it open access was displayed, and tis came from Saarland University. ‘’’Source:’’’ (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)

I aimed to answer the following questions regarding our database:

• Scientific quality of the database: (answered on October 1st by Quinn)

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: This database seems to have very strong coverage of the targets and pathways of mRNAs, but has not information on the mRNAs themselves. While this does align with what the database claims to cover, information on the mRNAs themselves would allow for a more full coverage of the field. Source: (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 with 14,773 experimentally validated target genes and 19281 predicted targets genes. Also a total of 12,875 biochemical pathway categories. As for Mus musculus, there are 1,933 miRNA covered and 9,741 biochemical pathways categories. Source: (https://mpd.bioinf.uni-sb.de/overview.html) (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
     • 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) in regards to target genes, and functional pathways for mRNAs to show how they function. Source: (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. Source: (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. Source: (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. Source: (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. Source: (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 that gives actual general information on each mRNA, 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. Finally, the websites KEGG, Reactome, Biocarta, Small Molecule Pathway Database, and National Cancer Institutes Pathway Interaction Database provide the information for the various biological pathways in the database. However, miRPathDB seems to fill a need by being a database that brings a lot of this scattered information to one place. Source: (https://wiki.nci.nih.gov/pages/viewpage.action?pageId=315491760), (https://www.ncbi.nlm.nih.gov/pubmed/19948758), (http://www.biocarta.com), (http://reactome.org), (http://www.genome.jp/kegg/pathway.html), (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. And several of their source databases have been updated since them. Source: (https://mpd.bioinf.uni-sb.de/documentation.html) (http://www.genome.jp/kegg/pathway.html) (http://reactome.org/cgi-bin/toc?DB=gk_current)

• General Utility: (answered on October 1st by John)

1. Whenever a search is performed for an miRNA molecule, the database provides a link to that molecule from the following sites: (http://www.mirbase.org/). It also directs you to a link that tells you what tissue that molecule might be located in using the following site: (https://ccb-web.cs.uni-saarland.de/tissueatlas/patterns). NOTE: It will link you to these databases whether or not you search a mouse or human miRNA. Sources: (https://mpd.bioinf.uni-sb.de/mirna.html?mirna=hsa-miR-1976&organism=hsa), (https://mpd.bioinf.uni-sb.de/mirna.html?mirna=hsa-miR-1976&organism=mmu)
2. It is very convenient to browse the data since it is organized first by species (human or mouse), then since the database is organized in a matrix, you can view the database and search through it by either the individual MiRNA and what pathways it is involved in or the pathways that contain the given kind of MiRNA.Source: (https://mpd.bioinf.uni-sb.de/pathways.html?organism=hsa)
3. It is somewhat convenient to download the data. The raw data is first given in both .tar.gz format and .zip on a designated page. While .zip is the standard way to compress a file, a .tar.gz acts as a container for compressed files and unless you are using Linux or MacOS, you need a software to open it. Finally, each of the queries can be downloaded into a new spreadsheet in either .xlsx or .csv format, both of which are standard formats. Sources: (https://mpd.bioinf.uni-sb.de/download.html), (https://mpd.bioinf.uni-sb.de/pathway.html?database=KEGG&pathway=MicroRNAs%20in%20cancer&organism=hsa)
4. I would say that the website is extremely well organized. It contains a very detailed tutorial in both a web page form and a .pdf download. The search options are very well-organized since they are separated by species, and the results can be either by pathway or by molecule. When I ran a query for the molecule "hsa-miR-1976" for example, two tables were returned that contained well organized-data that had their own search queries. Source: (https://mpd.bioinf.uni-sb.de/mirna.html?mirna=hsa-miR-1976&organism=hsa)
5. There are no restrictions on access nor is there a license agreement to use the database. Source: (https://mpd.bioinf.uni-sb.de/about.html)

• Summary judgment: (answered on October 2nd by Quinn)
  1. Would you direct a colleague unfamiliar with the field to use it? Answer I would definitely not direct a colleague unfimiliar with the field of miRNA to this website. This website has a very specific function and thus contains very specific data that is only useful to a trained professional that understands how to use the data. (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)
  2. Is this a professional or hobby database? Answer: Branching off of the previous answer, this is most certainly a professional database. The data is so specific and narrow that it really only serves a purpose for a professional who needs this kind of information for research purposes. (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)

Building the Powerpoint

After we had both individually researched the answers to our questions, we met for multiple hours on the afternoon of October 2nd to go over the information we have found. After discussing our thoughts on the database, and deciding on how to best present the information, we started a presentation on Google Slides. We began working on the slides together during the remaining time we had together. We then broke up the remaining slides to complete separately in the evening. Through the Chat option on Google Slides and text messaging, we stayed in contact about our progress as we finished the project. Finally, we planned to meet a bit before class on October 3rd to run through the presentation once together.

Submission

Media:Quinn_Lanners_and_John_Lopez_Biological_Databases_evaluation_of_miRPathDB_Database.pptx

Acknowledgements

Quinn Lanners

1. Quinn Lanners and John Lopez would like to thank each other for doing their part in the group project. By meeting once outside of class, and staying in contact throughout, we were able to work well together as a team.
2. Google Slides for providing an effective platform from which to work together simultaneously on the presentation.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Qlanners (talk) 22:28, 2 October 2017 (PDT)

John Lopez

I worked with my partner Quinn Lanners in class Tuesday to pick out our gene and Thursday to organize how we would do the questions. I decided to solve the General Information and General Utility questions, while Quinn would solve the Scientific Utility and Summary questions. By the time we met up on Monday, October 2nd, we had all of the questions finished and began to work on the presentation that day. Quinn set up the presentation, title, and outline. We corresponded after our meeting to finish the powerpoint due to Google Drive. I worked on the slides that I would present in class, and Quinn worked on his. We met before class on Tuesday, October 3rd, in order to rehearse the presentation.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Johnllopez616 (talk) 23:02, 2 October 2017 (PDT)

References

Backes, C., Kehl, T., Stöckel, D., Fehlmann, T., Schneider, L., Meese, E., … Keller, A. (2017). miRPathDB: a new dictionary on microRNAs and target pathways. Oxford Academic. Retrieved on October 1, 2017 from https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target
LMU BioDB 2017. (2017). Week 5. Retrieved October 1, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5
miRPathDB. (2016). Retrieved on October 1, 2017, from https://mpd.bioinf.uni-sb.de/documentation.html

QLanners Links

Main Page
User Page
Assignment Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14 | Week 15
Journal Entry Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14 | Week 15
Shared Journal Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10
Group Project Page: JASPAR the Friendly Ghost

Individual Journal Entries and Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14
• Week 15

Class Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14
• Week 15

Class Weekly Journal Entries / Project Weekly Journal Entries

• Class Weekly Journal 1
• Class Weekly Journal 2
• Class Weekly Journal 3
• Class Weekly Journal 4
• Class Weekly Journal 5
• Class Weekly Journal 6
• Class Weekly Journal 7
• Class Weekly Journal 8
• Class Weekly Journal 9
• Class Weekly Journal 10
• Class Weekly Journal 11
• Project Journal Week 12
• Project Journal Week 14
• Project Journal Week 15

My Page

• My User Page