1. miRPathDB: A Specialized Professional Database with Upkeep Concerns
John Lopez
Loyola Marymount University - Computer Science
Quinn Lanners
Loyola Marymount University - Applied Mathematics
BIOL/CMSI : Biological Databases
Seaver 120
10/3/2017

2. Outline General Information on the database
General utility of the database to the scientific community
Scientific Quality of the database

3. Outline General Information on the database
General utility of the database to the scientific community
Scientific Quality of the database

4. miRPathDB Provides Information on miRNA’s Target Genes and Involvement in Biological Pathways
microRNA (miRNA): short RNA sequence that affects gene expression (Cannel, 2008)
miRNAs have target genes and are involved in biological pathways
Target genes (miRPathDB)
Biological Pathways (National Human Genome Research Institute)
Genes that are repressed by the binding of miRNA to mRNA
Determined experimentally and through statistical prediction
Series of steps that create cellular product/change

5. The Center for Bioinformatics at Saarland University Constructed miRPathDB and Maintains It
In Saarbrücken, Germany
Non-profit, public research university with an emphasis on computing. (Saarland University, 2017).
Provided all known funding for the project. (Backes et al., 2017)
Allows the funding for it to be open-access (Backes et al., 2017)
Center for Bioinformatics - Where researchers for the project came from (miRPathDB) (Backes et al., 2017)

6. miRPathDB Uses Information From Several Databases
Link:
Several primary database sources
End result can be known as “metadata” (Backes et al., 2017)
Curated electronically using the GeneTrail2 C++ library and GNU Parallel shell (Backes et al., 2017)

7. Outline General Information on the database
General utility of the database to the scientific community
Scientific Quality of the database

8. https://mpd. bioinf. uni-sb. de/mirna. html

9. For a Scientist, This Site is Very User Friendly
If you know what you are looking for, the site is very easy to navigate. However, miRNAs and pathways are the only purposes of the site, making it difficult for users without prior knowledge on the subject. (miRPathDB) (Backes et al., 2017)
The website contains a very detailed tutorial in both a web page form and a .pdf download. (miRPathDB) (Backes et al., 2017)

10. Browsing and Downloading Data is Easy
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. Each of the queries can be downloaded into a new spreadsheet in either .xlsx or .csv format, both of which are standard formats. (miRPathDB) (Backes et al., 2017)
Because the data can be organized into a matrix, it is easy to navigate and sort by purpose. (miRPathDB) (Backes et al., 2017)

11. miRPathDB Relies Heavily Upon Other Databases
When a miRNA search is performed, two of the three links returned are other databases. The first, miRBase, is a database dedicated to miRNAs. The second, Tissue Atlas, relates to the tissues containing this molecule. The search works for both mouse and human miRNA. (miRPathDB) (Backes et al., 2017)

12. Outline General Information on the database
General utility of the database to the scientific community
Scientific Quality of the database

13. While Limited in Scope, miRPathDB Covers its Content Domain Well
Covers information on miRNAs targets and involvement in significant pathways (miRPathDB) (Backes et al., 2017)
Homo sapiens
2,599 miRNA
34,054 target sets (14,773 experimentally validated & 19,821 predicted)
12,875 biochemical pathway categories
Mus musculus
1,933 miRNA
9,741 biochemical pathway categories

14. miRPathDB compiles information to help study miRNA targets and involvement in biological pathways
Knowledge on miRNA has increased dramatically in recent years (Backes et al., 2017)
miRPathDB allows for the study of miRNAs target genes and their role in biological pathways (Backes et al., 2017)
Compiles information scattered across a variety of sources
Provides three ways to sift through data
miRNA focused
Pathway focused
Interactive heat maps

15. https://mpd.bioinf.uni-sb.de/mirnas.html?organism=hsa

16. https://mpd. bioinf. uni-sb. de/mirna. html

17. https://mpd. bioinf. uni-sb. de/mirna. html

18. https://mpd.bioinf.uni-sb.de/pathways.html?organism=hsa

19. https://mpd. bioinf. uni-sb. de/pathway. html

20. https://mpd. bioinf. uni-sb. de/pathway. html

21. https://mpd.bioinf.uni-sb.de/heatmap.html?organism=hsa

22. https://mpd.bioinf.uni-sb.de/heatmap.html?organism=hsa

23. https://mpd.bioinf.uni-sb.de/heatmap.html?organism=hsa

24. https://mpd.bioinf.uni-sb.de/heatmap.html?organism=hsa

25. Infrequent Updates a Point of Concern for miRPathDB
Unable to find launch date or update frequency (miRPathDB)
Significant time since last update from various data sources (miRPathDB)

26. miRPathDB: A Specialized Professional Database with Upkeep Concerns
miRPathDB is a secondary database that covers information about miRNAs target genes and involvement in biological pathways
The specialized nature of miRPathDB make it is easy to navigate for the professional user, but difficult for the average user
While thorough in covering its content domain, infrequent updates hinder the databases’ reliability

27. 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 dictionary-on-microRNAs-and-target
Cannel, I.G., Kong, Y.W., & Bushell, M. (2008). How do microRNAs regulate gene expression. Pubmed. Retrieved on October 2, 2017, from
miRPathDB. (2016). Retrieved on October 1, 2017, from sb.de/documentation.html

28. References cont.
National Human Genome Research Institute (2015). Biological Pathways. Retrieved on October 2, 2017, from pathways-fact-sheet/
Saarland University. (2015). Mission Statement. Retrieved on October 2, 2017, from