Using the Human Phenotype (HPO) Browser
Using the Human Phenotype (HPO) Browser
The Human Phenotype (HPO) Ontology is a community effort to provide standard terms for annotating human phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Selected terms are linked to a Human - Mouse Disease Connection query for the term and displays the human diseases and the high-level phenotype terms associated with the term, the human genes associated with those diseases and their mouse orthologs.
This help document answers the following questions about the Human Phenotype (HPO) Browser:
See also:
The Human Phenotype Ontology has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Organizing the phenotype terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of phenotypes from multiple perspectives.
Use the Browser to find vocabulary terms that may be used in annotations of phenotypic data. You can choose a term or HPO ID here to improve your searches with the Human - Mouse: Disease Connection form. Selected terms in the HPO Tree View link to a Human - Mouse Disease Connection query for the term and displays the human diseases and the high-level phenotype terms associated with the term, the human genes associated with those diseases and their mouse orthologs.
You can either browse or search from the HPO Browser. You can browse by clicking on terms in the HPO Tree View. This shows a term's place in the hierarchy, provides links to all diseases annotated to a selected term, and updates the HPO Term Detail section of the page with the selected term's parent terms, ID, definition, and any synonyms associated with the phenotype term. Searching requires entering a text string in the HPO Search box. This brings up an autocomplete list displaying all matches.
To browse the vocabulary, click a term in the Tree View or a parent term in the Term Detail section until you find the desired phenotypic term. A black triangle at the beginning of a term indicates the term has subterms. You can expand branches by clicking on a term or its preceding triangle. If you click on a term, this also updates the HPO Term Detail section. You can collapse branches by clicking on the downward-pointing black triangle. You can also click on the triangles to navigate the branches without updating the Term Detail section. You can copy term IDs into the Disease or Phenotype (IDs) field on the Human - Mouse: Disease Connection to search for data associated with this term.
The HPO Search field accepts any text string and searches for all terms containing that string and any synonyms. To do this:
Select a term in your search results to automatically update the HPO Term Detail and HPO Tree View sections on the right. Use the Clear button to start a new search.
| HPO Search | The search finds all phenotype terms that contain all of your search terms and displays a ranked list of those terms. Click on a term to update the HPO Term Detail and Tree View sections of the page with the appropriate phenotypes and the selected term highlighted in blue. | ||||||||||||
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| HPO Term Detail |
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| HPO Tree View | The main phenotype headings are shown beneath the section header. The number of diseases annotated to the selected term is shown. Child terms are shown beneath the selected term in the tree view. You can collapse or expand branches by clicking on a triangle. When you select a new term, it is highlighted in blue and the Term Detail section is updated.
Click on the number of diseases with annotations link to run a Human - Mouse Disease Connection query for the term. |
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 "Is-a" Relationship | Indicates that the term is an instance or type of the more general term(s) above it in the tree. For example, Uveitis is an Abnormality of the uvea and an Inflammatory abnormality of the eye. | ||||||||||||
 | A black triangle preceding a term in the Tree View indicates that the term has children. Click on the triangle to see the additional paths. You can collapse branches by clicking on the downward-pointing triangles. Unlike clicking on a term, clicking on a triangle does not update the selected term. | ||||||||||||
| # diseases with annotations | Number of diseases annotated to the term and its descendants. Click this link to to run a Human - Mouse Disease Connection query for the term. |
Selected terms are linked to a Human - Mouse Disease Connection query for the term and displays the human diseases and the high-level phenotype terms associated with the term, the human genes associated with those diseases and their mouse orthologs. In your HMDC results, use the "Click to modify search" button and you will have the option of adding related Mammalian Phenotype terms to the search. For more details see: How do I interpret the (HMDC) query results?
The Human Phenotype Ontology is developed by Peter Robinson's group. Additional terms or revisions may be requested through their issue tracker at GitHub.