The OMIM® Explorer: Phenotype + Genotype = Diagnostics + Discovery
OMIM® Explorer:
Rapid integration of phenotype with genotype to aid in differential diagnostics of genetic disease, molecular variant prioritization, and novel gene-phenotype association discovery.


Identify diseases by annotated phenotype or gene, or by OMIM Name/ID.
Import
Upload a previous OMIM Explorer session file to continue your work.
Export
Download your current work in a shareable OMIM Explorer session file.

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Recessive Logic: When zygosity is supplied as "Hom" or "Het" in optional "ZYGOSITY" column of uploaded VCF, exclude in diagnostic and gene discovery tables the heterozygous genes with only 1 variant when those genes are associated in OMIM with only recessive diseases.

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NOTE: Initial loading of input menus can last up to 60 seconds on high-speed internet connections, and may temporarily slow browser tab functionality. Please do not refresh.
Note: Including as many descriptive phenotypes as possible helps optimize rankings and break ties. Alternatively, submit a text file containing a list of HPO term IDs (1 ID per line) to add phenotypes to query:
Categorize selected phenotypes.
Select phenotypes in the "Toggle" tab to categorize them as "Mandatory."
Select phenotypes and toggle their "Mandatory" status to adjust their specificity. Example: "cortical cataract" has a higher specificity than "abnormality of the lens."
Categorization modifies plots and summary tables ONLY, NOT similarity estimates.
Dynamically generated links to searches for selected phenotypes on external web researches.

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NOTE: Initial loading of input menus can last up to 60 seconds on high-speed internet connections, and may temporarily slow browser tab functionality. Please do not refresh.
Submit a set of RARE variant genes to be appended to the gene filter (single patient only). Click the "Variants" tab to view more details about uploaded genes. Supports hg19 VCF and single-column CSV files.
Note: A 1% maximum MAF (minor allele frequency) filter, computed across the ExAC database, is automatically applied to variants in uploaded VCFs.
VCF file documenting variants in an otherwise healthy individual (Manuel Corpas). Submitting a query using Kleefstra syndrome phenotypes* transitively (via maximum annotated similarity score) ranks as #1 the VCF's variant gene EHMT1, which has been previously documented as a gene in which variants can cause Kleefstra syndrome. *Known Kleefstra syndrome phenotypes include macroglossia, autism, obesity, muscle weakness, microcephaly, and intellectual disability, among others. Click here to directly select these phenotypes in a new window.

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NOTE: Initial loading of input menus can last up to 60 seconds on high-speed internet connections, and may temporarily slow browser tab functionality. Please do not refresh.


Select an OMIM point of interest on the GLOBAL 2D disease map and use the controls to visually investigate the phenotypic attributes of that region.


Configure semantic similarity and visualization settings for local/top-disease and global/all-disease maps.


Publications: For work generated using OMIM Explorer, please reference the Genome Medicine article entitled "A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics."

Double-click video to view fullscreen.

Visit the OMIM Explorer YouTube Channel to view more introductory videos and step-by-step tutorials for various use cases.

  • Is there an API for programmatic execution of OMIM Explorer queries?
    Currently, there is no API for OMIM Explorer, because it does not align with the inherently iterative nature of the collaboration between physicians and exome curators in the clinical diagnostic process for which OMIM Explorer was primarily designed to provide support. Notwithstanding this, an API may be developed in the future, particularly for programmatic implementation in more discovery-related contexts.
Disclaimer: Not intended for direct clinical application. All OMIM Explorer results are systematically-generated suggestions that may require additional confirmation. This validation is the responsibility of the user. Neither Baylor College of Medicine nor any individual involved in the construction of OMIM Explorer is responsible for clinical actions that may result from the use of this software. By using this tool, the user assumes all responsibility for any information that may be generated.
Ā©2015 Shaw Laboratory,
Baylor College of MedicineĀ®
Questions or Comments? Contact the developer,
or Associate Professor and thesis supervisor
Enter a description of the queried case. Use this as a starting point for phenotype extraction, or for documenting diagnostic progress.
Suggestions generated via the Bio-LarK Concept Recognizer.

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Differential Diagnosis Curation
Hover cursor over the OMIM Disease Map to the left to visually explore the known clinical phenotype presentations and genes containing variants causal of disease. Click to select a disease.
Details Under Cursor
Phenotypic comparison of
Local map diseases considered for differential diagnosis:
Variant data on radar
Show radar ranks
Limit radar map to diseases w/ known genetic causes

Approximate
global
map

Details of diseases within radially-selected region of 2d disease map. (global view ONLY)
Details of phenotypes annotated to OMIM diseases within region selected in 2d disease map. (global view ONLY)
Rare phenotypes have high IC, and common terms have low IC. The informativeness, or information content (IC), of a phenotype is defined as the negative log of that phenotype's frequency among all diseases.
Select a disease class to highlight its constituent diseases below.

Approximate
disease
map

Constituents of HDN disease class selected above. (Reference: Goh, 2007)
Click here to view constituent diseases on the OMIM website.

Submit a phenotype query via the search panel to generate similarity rankings for OMIM diseases and variang genes.
Submit phenotype query to generate gene ranks.
Submit phenotype query to generate.
Suggestions are rarest phenotypes of diseases most similar to query, sorted by relevance.
Select genes to generate.
Suggestions are phenotypes annotated to diseases meeting gene filter
Select phenotypes to generate.
Suggestions are genes annotated to diseases meeting phenotype filter. ("Search -> Phenotype -> Select OR Sort")
These are NOT molecular diagnostic suggestions. Please refer to the "Differential Diagnosis" section for molecular diagnostics suggestions, which are computed via semantic similarity calculations.
Select diseases in the "MIM ID" subtab of the "Input" tab to the left to view their respective phenotypic and genotypic annotations, similarities to each other, and similarities to any queried phenotypes.
Select at least 2 diseases to generate a heatmap of Resnik similarities computed between all pairs.

Submit query to display candidate gene contacts in training gene network.

Upload variant genes to view input summaries.
(Select "Input" -> "Gene" -> "Upload" in the left navigation panel.)

Click the guide buttons above to perform phenotype-driven, semantic clinical diagnostics and discovery.

Start
Disclaimer: Not intended for direct clinical application. All OMIM Explorer results are systematically-generated suggestions that may require additional confirmation. This validation is the responsibility of the user. Neither Baylor College of Medicine nor any individual involved in the construction of OMIM Explorer is responsible for clinical actions that may result from the use of this software. By using this tool, the user assumes all responsibility for any information that may be generated.
Watch introduction video (example screenshot below) | Read article in Genome Medicine
Questions or Comments? Contact the developer,
or Associate Professor and thesis supervisor

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Watch introduction video (example screenshot below) | Read article in Genome Medicine
Questions or Comments? Contact the developer,
or Associate Professor and thesis supervisor