New Monarch Initiative Website
The Monarch Initiative offers an integrative data and analytic platform connecting phenotypes to genotypes across species, bridging basic and applied research with semantics-based analysis. Our newly redesigned website is now live at monarchinitiative.org. The new interface offers a simplified format for accessing and exploring our data using names or identifiers to find phenotypes, diseases, genes, publications, variants, and models of human disease.
The Monarch database integrates information from phenotype-related resources, allowing users to establish connections among biological entities of interest, such as genes, genotypes, gene variants (including SNPs, SNVs, QTLs, CNVs), models (including cell lines, animal strains, species, breeds, as well as targeted mutants), pathways, orthologs, phenotypes and publications. The information is organized using ontologies, rather than free text in isolation. This means that features of the ontology can be used to assist in search — for example, finding a disease of interest using a synonym, or using the hierarchical organization of a phenotype ontology to group annotations.
On the home page, the ‘Search’ bar lets users navigate directly to terms suggested via autocomplete, or explore more options through the results tables. The main page for each phenotype, gene, or disease, the ‘Overview’ tab, offers a summary of all available information in Monarch’s knowledge base. For example, when users enter the name of a disease such as ‘Pierpont syndrome’ in the search box, they will be directed to the overview page for this disease, linked here, for easy exploration. This page offers a summary of all available information in the integrated knowledge graph of the Monarch database. The figure below shows that users can explore all available data using a menu of options shown on a panel on the left (in green), while the information is updated on the main panel on the right (in white). As users browse the page, they learn that ‘Pierpont syndrome,’ a rare subcutaneous tissue disorder, is characterized by 59 phenotypes, such as ‘prominent subcalcaneal fat pad’ (a term in HPO, with identifier HP:0032276), among many others. In the figure below, information integrated from the OMIM and Orphanet databases, as well as a number of publications (see panel on the left), also support the association of a mutation in one gene, TBL1XR1, as the cause of ‘Pierpont syndrome.’
The new site includes an updated version of our text annotation tool (available from the ‘Tools’ menu) which allows users to automatically mark up phenotypes, diseases, anatomical terms, genes and other entities found in text from publications, and it also allows users to conduct a ‘Phenotype Profile Search’ using the collection of terms marked up on the text.
Our new website is designed to help YOU, our users. Please don’t hesitate to contact us with any questions or feedback. We look forward to hearing from you!
