Difference between revisions of "The Monarch Initiative"

Revision as of 21:30, 2 October 2017

This is Nicole Kalcic's and Dina Bashour's Week 5 assignment.

To begin, we found our database by browsing the information via [| Descriptions of new online databases in the 2017 NAR Database issue]. After settling on [| The Monarch Initiative], we split up the questions below. Nicole Kalcic completed the first and second bolded sections. Dina Bashour completed the second and fourth bolded sections. The finished assignment was checked by both of us to insure there were no mistakes in our own sections or the other person's sections.

• General information about the database
  1. Link to the database: https://monarchinitiative.org
  2. The database focuses on human disease related genotypes/phenotypes. (https://monarchinitiative.org/page/about)
     1. The database uses model organisms for phenotype comparison within/across species. (https://monarchinitiative.org)
     2. The information on Monarch is considered a secondary source because it is curated from established “databases, spreadsheets, delimited text files, XML, JSON, and Web APIs”. This work is done personally by the staffed individuals at the database’s contributing institutions, which are listed in question number three. (https://monarchinitiative.org/page/about)
  3. The Monarch Initiative is maintained by several institutions, including Oregon Health & Science University, Lawrence Berkeley National Laboratory, The Jackson Laboratory, Charité - Universitätsmedizin Berlin, Queen Mary University of London, Garvan Institute, Renaissance Computing Institute - University of North Carolina at Chapel Hill, and University of Pittsburgh. More information about the contributing individuals at each institution can be found by clicking on the hyperlink. (https://monarchinitiative.org/page/team)
  4. The institutions found funding for the database through a National Institutes of Health Office of the Director Grant, as well as through the National Institutes of Health Undiagnosed Diseases Program. (https://monarchinitiative.org/page/team) (https://www.genome.gov/27544402/the-undiagnosed-diseases-program/)
• 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?
• General utility of the database to the scientific community
  1. Each page of information contains a Uniform Resource Identifier link. The data sources used for URIs can be found at https://monarchinitiative.org/about/sources. There are currently thirty sources integrated into the database.
  2. It is generally convenient to browse the data. As stated, if you search “Parkinson’s”, a single query will retrieve all data from the system that is considered relevant. However, when reading “The Monarch Flow Data”, many of the links describing the process were broken. This was not a huge issue, as I was able to find the described pages on my own, but it could easily be fixed so that the user has a more immediate trust in the database. (https://monarchinitiative.org/page/about)
  3. Is it convenient to download the data?
     • In what file formats are the data provided?
     • Are they standard or non-standard formats?
  4. 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?
  5. Access: Is there a license agreement or any restrictions on access to the database?
• Summary judgment
  1. Would you direct a colleague unfamiliar with the field to use it?
  2. Is this a professional or hobby database?

Acknowledgements

• Nicole Kalcic and Dina Bashour communicated via text and met in person to complete the different requirements of this assignment.
• While we worked with the people noted above, this individual journal entry was completed by us and not copied from another source.

Nicolekalcic (talk) 14:22, 2 October 2017 (PDT)

References

• LMU BioDB 2017. (2017). Week 5. Retrieved October 2, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5
• https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database
• https://monarchinitiative.org
• https://www.genome.gov/27544402/the-undiagnosed-diseases-program/