The Monarch Initiative

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This is Nicole Kalcic's and Dina Bashoura'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 Bashoura 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.

Database Evaluation

  • General information about the database
  1. Link to the database: https://monarchinitiative.org
  2. The database focuses on a cross-species examination of diseases, genes, and phenotypes. (https://monarchinitiative.org/page/about)
    • The database uses model organisms for phenotype comparison within/across species. (https://monarchinitiative.org)
    • 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. The content appears to completely cover its content domain.
    • The database is composed of 5 records, overview, diseases, phenotypes, models, and genes, with each containing a field of information associated with their specific record. (https://monarchinitiative.org)
    • The owners of the database provide a ven diagram in the corresponding paper illustrating the phenotypic coverage of all 19,008 human protein-coding genes. This diagram shows that 51% of human protein-coding genes have at least 1 phenotype association in humans, 58% have orthologs with causal phenotypic associations reported in at least one non-human model, 40% have annotations both in human and non-human orthologs. This shows that 89% have phenotypic associations from humans and/or non-human orthologs and 11% have no annotations in any species. Monarch Initiative Corresponding Paper
  2. There are 7 species in the database: human, mouse, worm, fly, zebrafish, dog, and cow. (https://monarchinitiative.org/model)
  3. The content of this database is useful in that it shows diseases described with phenotypes, gene variations associated with certain diseases, phenotype comparisons that suggest models, and models that suggest candidate genes. Each category of information has an interactive graph used to display the information in a concise and easily readable manner. (https://monarchinitiative.org/model)
  4. The information can be used by the scientific community and the content is timely. The Monarch Initiative integrates the biological information using semantics, and presents it in a novel way, leveraging phenotypes to bridge the knowledge gap. It allows for the phenotypic comparison both within and across species, hopefully aiding in the improvement of biomedical research. (https://monarchinitiative.org/page/about)
    • There are other databases that provide cross species examinations but not any that contain the specific species used in this database. Databases like WormBase and 4DXpress both provide a cross-species comparison but The Monarch Initiative presents the information in a very clear and effective way with the use of the interactive graphs while these other databases do not. The other databases also either do not compare the same information as the Monarch Initiative or they allow for comparisons using blast or by inputting your own DNA sequences. (http://www.wormbase.org/#0125-34-5) (http://4dx.embl.de/4DXpress/guest/login.do)
    • The Monarch Initiative first went online on July 10, 2015. (https://monarchinitiative.org/page/releases)
    • The database is updated roughly once a year, offering the opportunity to provide feedback or submit questions, suggestions, problems, or concerns to the Monarch team. (https://monarchinitiative.org/page/releases)
    • The most recent update was in September of 2017, updating the data both on the website and on their app. (https://monarchinitiative.org/page/releases)
  • 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. As someone who is not very familiar with computer science outside of this class, I would say that it is possible to download data but it is not the easiest process. You can locate downloads under the "About" tab and then by clicking on "Data Downloads". You will be taken to this page: https://archive.monarchinitiative.org/latest/. The latest downloads will come up with corresponding dates and times. A lot of the downloads are presented in .tgz format. Many of the downloads further open up into .txt files, but you would not be able to do a successful download with some knowledge of the computer or a few google searches in order to understand the download process when not in .zip.
    4. I believe a naive user could easily navigate this website. It is well organized, and you can quickly find and click on "About Monarch" under the "About" tab. The "About Monarch" page takes you through the background, the curation process of the data, and what you should expect to find upon doing a search. Other than that, the website is organized with clear headings, and it uses a design that is updated and colors that help direct and engage a user. If I search "Parkinson's", everything on the database relevant to Parkinson's will come up, and I can easily sort through the information and find the disease or phenotype that I am looking for. (https://monarchinitiative.org/page/about)
    5. There are no restrictions on access to this database. The bottom of their webpage states that it is licensed under a Creative Commons Attribution 3.0 License, except where forbidden by the original sources. (https://monarchinitiative.org/page/about)
  • Summary judgement
    1. I would direct a colleague unfamiliar with this site to view the database because I found it to be very easy to follow and a useful tool for performing a cross-species examination. I was originally unfamiliar with this site but was able to quickly and easily become acquainted with what it can do and what it has to offer.
    2. This could be either a professional or hobby database. The database can surely assist in professional usage but can also serve as a reference for someone who wants to perform a cross-species comparison on a certain gene, phenotype, or disease for recreational usage.

Submission

File:The Monarch Initiative.pdf

Electronic Notebook

Once a database was chosen for the completion of this assignment, Nicole and I split up the work in order to be most efficient. While she completed the "General information about the database" and the "General Utility of the Database to Scientific Community", I completed the "scientific quality of the database" and the "summary judgement" portion of the assignment.
Most of the information could be found on the about page, but some information was taken from other sections of the database. We searched through the database individually to complete our assigned sections and together gathered the information onto this wiki page.

Acknowledgements

  • Nicole Kalcic and Dina Bashoura communicated via text and met in person to complete the different requirements of this assignment.
  • We looked at the formatting of the MiRPathDB page in order to help construct ours.
  • 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) Dbashour (talk) 15:26, 2 October 2017 (PDT)

References

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