The MouseFinder Tool

What is it?

MouseFinder is a tool for exploring phenotypic similarities between Mendelian diseases recorded in OMIM and mutant mouse lines curated by the MGI group.

The goal of this comparison is to identify novel candidate genes for diseases where the underlying molecular mechanism is currently not known.

The disease and mouse data is compared semantically using OWLSim.

To achieve this we take advantage of Human Phenotype Ontology (HPO) and Mammalian Phenotype Ontology (MPO) annotated datasets and the logical decompositions of HPO and MPO using the Phenotype and Trait Ontology (PATO) to describe qualities and a variety of ontologies such as

Gene Ontology (GO),
Mouse Pathology (MPATH),
Chemical Entities of Biological Interest (CHEBI),
Foundational Model of Anatomy (FMA) and
Mouse Anatomy (MA)

to describe the entities.
The UBERON unified metazoan anatomy ontology is used to map between the species-specific anatomical ontologies.


To use MouseFinder, choose a disease of interest by searching/browsing by OMIM ID, name or HPO annotation or by gene name where a disease-gene association has already been made.

Once you have chosen a disease, the ranked lists of mouse matches are shown along with any known OMIM gene associations and disease models asserted by MGI.
Ranking is based on pairwise comparisons of all the HPO and MPO annotations for each disease and mouse model respectively. Each HPO-MPO match is scored either by the Information Content (IC) or Jaccard Similarity (simJ) and an overall scores for each disease-mouse comparison is calculated as either the average or maximum of the IC or simJ scores.

The results from these avgIC, maxIC, avgSimJ and maxSimJ rankings are displayed in separate tabs in the results window. To view the individual phenotype annotations for a human-mouse match, along with the matching terms, expand the detail in that results row.

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HP (Human Phenotype ontology) / MP (Mouse Phenotype ontology) Info

This should
(1) give info about vesions of ontologies used

(2) say how many terms in HP and MP ontology, respectively; and how many terms in HP can be translated/mapped to MP terms.

(3) The dated version of mapping software

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Navigating HP Ontology Tree for Mouse Phenotype

Adjusting width of the viewing area: slide the split bar on the right side of the tree box to the left and right to adjust the width of the tree viewing area and the results pane on the right simultaneously.

Hiding tree view: click on the toggler in the middle of the split bar, you could hide the tree view and fully expand the results pane.

The gray-out HP terms indicate that currently no mouse phenotype translation/mapping is available.

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Search Help

Autocomplete feature

Type in at least one alphanumeric character (for HP or OMIM ID, omit the prefix) and you will be prompted a list of OMIM / HP or gene names (eg, OM: xxxx, HP: xxxx OR GN: xxxx) from which you could narrow down your search.

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About found mouse models of an analysis matching OMIM, MGI curations

The <OMIM gene, mouse model curation> tab summarizes a list of MGI curated mouse models and OMIM curated human gene symbols (when available), which match our analysis results as shown in the analysis column of each table.
For OMIM gene symbols with multiple synonyms, the ones matching mouse symbol in the results set (case insensitive) will be boxed in pink.

If there is any model in the analysis (avg ic / max ic) which matches either one of the OMIM (symbol match) or MGI curation (allelic composition match), the text of the analysis tab will be shown in green.

The matching models in the analysis tab will be marked with green ticks (indicating models matched by allelic composition) at the left side of the model rows or as pink boxes surrounding mouse gene symbols (indicating models matched by symbol).

OMIM disease and found mouse models
Case insensitive search