Using the Disease Ontology (DO) Browser
Using the Disease Ontology (DO) Browser
The Disease Ontology (DO) is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view DO terms, definitions, and term relationships in a hierarchical display.
This help document answers the following questions about the DO Browser:
See also:
The Disease Ontology is built on a Directed Acyclic Graph (DAG) structure. In a DAG, an ontology term can have more than one parent term. The Disease Ontology (DO), is a hierarchical standardized ontology that integrates vocabularies from MeSH, ICD, NCI's thesaurus, SNOMED, UMLS, Orphanet, EFO and OMIM. Its hierarchical structure permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating mouse model data to the level of detail known and for searching for this information using either broad or specific terms as search criteria.
You can browse the Disease Ontology hierarchy and for each selected disease term, find genes and mouse models associated with the term.
The top of the page shows the disease term, its DO ID, synonyms, Alternative IDs, linked when possible to the relevant source, and the term definition. This section also provides a link to the Alliance of Genome Resources (AGR) page for the disease term. AGR integrates data from 6 Model Organism Databases and the Gene Ontology (GO) Consortium. The founding database members of the Alliance are Flybase, Mouse Genome Database, Rat Genome Database, Saccharomyces Genome Database, Wormbase, and the Zebrafish Information Network.
The main body of the page provides 3 tabbed views,Term Details, Genes and Models. Term Details is the default selection.
Term Details: A portion of the Disease Ontology (DO) hierarchy is represented by three blue-boxed sections, and below this section, a graphical representation of the hierarchy. The middle box highlights the selected term—the term defined at the top of the page—and lists its sibling terms below. To the left are those terms' parent terms and to the right, the highlighted term's child terms—terms below it in the ontology hierarchy. Click on a term to refresh the page and make it the highlighted term and to see its parent and child terms, and at the top of the page, its DO ID, synonyms and definition.
A graphical representation of the hierarchy is displayed below the three boxes. As with the upper section, the selected term is highlighted in yellow and you can navigate the hierarchy by clicking on a term. Unlike the top section, though, sibling terms are only shown for the lowest level of the hierarchy. Place your cursor directly over an arrow to see the DO IDs for the linked terms. The selected term is presented first.
Genes: A list of all mouse and human genes where mutations in one or both species are associated with phenotypes characteristic of this human disease and its child terms in the DO hierarchy. Mouse and human icons categorize the associated genes by the following conditions:
The disease is associated with both the mouse and human homologs of the same gene. Mouse genes may appear in this section based on disease models that express homologs of the mouse gene.Mouse models involving mutations in the mouse gene or expressing homologs of the mouse gene are associated with this human disease. (OMIM and NCBI data currently do not associate this disease with the homologous human gene.)Mutations in the human gene are associated with this human disease phenotype. MGI may not contain evidence that a mutation in the mouse gene represents a model for this disease, if the mouse gene is homologous to a human gene associated with a disease, it is listed as a disease homolog.Links to additional information on genes, genotypes and phenotypes:
A separate table of Transgenes and other genome features developed in mice and used to to model this disease may appear beneath the main table. Transgenes and Other Mutations appears when at least one of the non-gene mouse markers is associated with this human disease.
Models: A table of all models with phenotypic similarity to the disease. Models are organized into the following categories:
Mouse models where at least one of the mouse genes and its homologous human gene are associated with this human disease. Mouse genes may appear in this section based on disease models that express homologs of the mouse gene.
Mouse models involving mutations in the mouse gene or expressing homologs of the mouse gene are associated with this human disease. (OMIM and NCBI data currently do not associate this disease with the homologous human gene.)Mouse models where none of the mouse markers are associated to the disease but at least one of the human homologs is associated with this human disease.| Disease Term | The disease term associated with the model. This column includes child terms of the selected term indicated at the top of the Disease Ontology Browser page. |
|---|---|
| Allelic Composition | Allele pairs that contribute to the genotype. Each allele is linked to its corresponding Phenotypic Allele Detail report. |
| Genetic Background | Mouse strains involved, if described. |
| Reference | The supporting reference linked by its MGI reference number to the MGI Reference Detail report containing the full citation. |
| Phenotypes | Links to the phenotypic details for the genotype. |
Yes. The Genes and Models tabs provide export options. Above the table of results, click on the Text File or Excel File icon. Your web browser will download a file of the results. The exported file will not contain the transgenic models.
Human gene to disease associations are from the Alliance of Genome Resources Homo sapiens associations disease file and include annotations from OMIM, RGD, NCBI curation, Gene Reviews, and Gene Tests. Human disease associations to mouse genes are from MGI curated data and are only made when the genotype of at least one mouse model allows for a clear gene to disease relationship to be determined.
The Disease References using Mouse Models links to a list of the references that discussed mouse models of the disease.
MGI uses the doid-merged.obo version of the DO ontology. This version includes asserted is_a relationships, is_a relationships derived from tissue/organ location information and additional OMIM cross-references from susceptibility relationships.