Our phenogrid tool visualizes phenotype comparisons across species, models, and other diseases.
We also have an API, which allows bioinformaticians and web developers to access the integrated Monarch data programmatically: https://api.monarchinitiative.org/api/. Our API supports complex queries, for example, finding mouse models of Parkinson’s disease, or all human genes associated with cleft palate phenotype, or a list of all vertebrate genes with either phenotype or disease associations. Helpful use cases and the code behind the API can be found here: https://github.com/biolink/biolink-api. Users can find and access our integrated data in multiple ways. For example, if you are interested in breast cancer data, you can search for ‘breast cancer’ on the web portal and see our breast cancer data overview page, you can view this data in JSON format, or you can use the API to find all genes associated with breast cancer in our system.
What is all this integrated data good for? Monarch has developed a clinical diagnostic tool, Exomiser, which is used to rank variants as being potentially disease causing. Exomiser is utilized extensively by the rare disease community, by the NIH Undiagnosed Disease Network, and by various commercial entities such as Cartegenia, and is the first example of a clinical diagnostic tool used to diagnose patients that leverages model organism data directly.
How can you join us on our data integration quest? Please use our tools and provide us with feedback! We are working on updating our Web Portal user interface this year, so we would like to know what features are useful (or not useful) for you and where we could improve. We would also like to hear from you if you have data that you’d like to share with us. Or, have you noticed data that we should have but don’t? Please let us know by emailing (info@monarchinitiative.org), tweeting at us (@MonarchInit), or sign up for our newsletter. We are also working on improving our data ingest documentation so that outside users can ingest their data into our system on their own; keep your eyes peeled for this implementation!
To support openness and data sharing, the Monarch data ingest source code, ontologies, and web application code are all openly available on Github (https://github.com/monarch-initiative/). We invite the scientific community to join us on our quest to improve disease diagnosis and discovery by sharing and integrating phenotype, genotype, and disease data from all species.
Monarch Initiative member groups: OHSU, Lawrence Berkeley National Laboratory, the Jackson laboratory, Renaissance Computing Institute, Queen Mary University of London, Charité - Universitätsmedizin Berlin, and the Garvan Institute. Joining this fall is our newest member, from the European Bioinformatics Institute. https://monarchinitiative.org/page/team