BioGPS Spotlight on RGD and RatMine

RatMine is one of several InterMine-based resources available as plugins in BioGPS. Unlike FlyMine and HumanMine (which are run by the InterMine team), RatMine is one of several resources available in the Rat Genome Database (RGD) offered by the Biomedical Informatics Program at the Medical College of Wisconsin. The Rat Genome Database is a well-respected and established resource for rat information. RGD’s Jennifer Smith kindly answered our questions about this excellent resource.

  1. In one tweet or less, introduce us to RGD and RatMine:
    RGD presents genetic, genomic, phenotype & disease data for rat, and mouse & human orthologs; RatMine extends queries to additional species.
     

  2. Who is your target audience?
    Our primary target audience is researchers using or considering the use of rat as a model, particularly for human disease. However, because of our extensive set of functional annotations across rat, mouse and human, and the tools we’ve developed for querying and analyzing that data, we have a wide range of users including academic researchers, pharmaceutical companies, clinical geneticists and bioinformaticians.
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  4. Why did you create your tool? At what point in RGD’s history was InterMine integrated for the creation of RatMine?
    We started developing RatMine in 2009, about 10 years after RGD began. RatMine was incorporated as an alternate view of the RGD data, to provide functionality that didn’t exist in RGD at the time, including the ability to create and save custom queries and lists, the availability of a variety of widgets such as the ontology annotation enrichment widgets, and the prospect of being able to use the InterMine functionality to link data from rat to additional species such as yeast, fly and zebrafish, with their extensive history as research models.
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  6. What makes RatMine unique and special?
    We believe that RGD’s data is what makes RatMine unique and special. At RGD, we incorporate and manually curate data across rat, mouse and human. In addition to comprehensively annotating rat genes, QTLs and strains, we annotate disease and molecular pathway associations for genes in all three species. Our pipelines augment our manual annotations with important information from other groups such as Gene Ontology (i.e. functional) annotations for mouse and human genes and a large corpus of human clinical variant data from NCBI’s ClinVar database, allowing us and our users to leverage the strengths of all three species.
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  8. What level of traffic does RatMine typically see?
    In combination, RGD and RatMine average over 10,000 users and 50,000 page views per month.
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  10. RGD seems to serve a thriving community of researchers. What is your greatest success story so far?
    The world of biology and genomics is rapidly changing as methods change, new data types emerge and the volume of data grows by leaps and bounds. We think our greatest success story is that in this shifting landscape we provide a comprehensive resource, not just of the various types of genomic data as our name implies, but also the core physiology and disease data for which rat is such an established model. We are able to highlight advances made by rat researchers worldwide, including the exciting advances made in genome editing in the rat, and link that to data from mouse research and human clinical studies, and feed it all into innovative tools for analysis.
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  12. What improvements are coming in the future for RGD? For RatMine?
    For RGD, here’s what we have coming up in the immediate future:

    • A “MyRGD” feature which will allow users to create accounts to save queries and datasets, and to add “watchers” to specific data items or data types and receive notifications when, for instance, a new functional annotation was added to their gene of interest, or additional genes, strains or QTLs were associated with a disease of interest
    • A Cytoscape-based protein-protein interaction data viewer whereby users can enter a gene or protein identifier, or a list of them, and view and/or download all of their interactions
    • Our next Disease Portal will focus on Hematologic Diseases and will feature genes, strains and QTLs with disease, phenotype, pathway and/or biological process associations related to hematologic diseases

    Farther down the road, we are also working on

    • A “Strain Portal” which will consolidate data on rat strains and highlight RGD tools that utilize strain-related data
    • A programming API to facilitate access to RGD’s data by other websites and tools

    For RatMine, future improvements include:

    • We are working with the InterMine group on a new query tool to obtain functional annotations from orthologous genes across seven species in a single interface
    • We will add RGD’s gene-chemical and gene-drug interactions to the data available in RatMine
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  14. Who is the team behind RGD and RatMine??
    The Principal Investigator for RGD is Dr. Mary Shimoyama. Dr. Mindy Dwinell is Co-Investigator. In addition, RGD has a close-knit team of six curators, four developers and a database administrator:

    RGD’s Research Scientists/Curators:

    • Stan Laulederkind, PhD
    • Tom Hayman, PhD
    • Victoria Petri, PhD
    • Jennifer Smith, MS
    • Monika Tutaj, PhD
    • Shur-Jen Wang, PhD

    RGD’s Developers:

    • Jeff De Pons (Bioinformatics Manager)
    • Marek Tutaj, MS
    • Jyothi Thota, MS
    • Omid Ghiasvand, MS
    • Stacy Zacher, MS (DBA)

Thanks to Jennifer Smith, for guiding us through these extremely useful and FREE resources. Be sure to check out the RatMine and the RGD plugins in the plugin library. If you use RatMine in your research, be sure to cite their publication:

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D743-50. PMID:25355511


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