Human Phenotype Ontology

Category Genomics>Genetic Data Analysis/Tools

Abstract The Human Phenotype Ontology (HPO) is a tool for annotating and analyzing human hereditary disease. The human phenotype ontology offers a computational tool that allows large-scale computational analysis of the human phenome.

The manufacturer has mapped nearly all clinical descriptions in the Online Mendelian Inheritance in Man (OMIM) database that are used more than once to terms of the HPO (contains over 8,000 terms representing individual phenotypic anomalies).

They have embedded these mappings into an ontological, multi-tiered structure that is described below and intend to continue refining and improving the HPO.

In the future, the annotations to the HPO will be extended to include chromosomal disorders.

Terms in the Human Phenotype Ontology -- Each term in the HPO describes a clinical abnormality. These may be general terms, such as Abnormality of the musculoskeletal system or very specific such as Chorioretinal atrophy.

Each term is also assigned to one of the three (3) ontologies, Organ abnormality, Inheritance and Onset and Clinical course. Most of the terms of the HPO belong to the Organ abnormality ontology.

The terms have an ID such as HP:0001140 and a name such as "Epibulbar dermoids". Some terms have definitions such as "An epibulbar dermoid is a benign tumor typically found at the junction of the cornea and sclera (limbal epibullar dermoid)."

The source of the definition is also indicated. Currently, the source is indicated as HPO:curators. Many terms have synonyms. Most of the synonyms are taken from OMIM entries, which were made over several decades without a controlled vocabulary.

For instance, "Epibulbar dermoid" is taken to be a synonym of "Epibulbar dermoids". The synonyms may also be useful for searches. The Organ abnormality ontology -- This is the main ontology of the HPO and contains descriptions of clinical abnormalities.

The level 1 children of Organ abnormality is formed by terms such as Abnormality of the musculoskeletal system and Hematological abnormality.

The Inheritance ontology -- This relatively small ontology is intended to describe the mode of inheritance and contains terms such as Autosomal dominant.

The Onset and Clinical course Ontology -- This ontology describes the typical time of onset of clinical symptoms and their speed of progression. It contains terms such as ‘Onset in childhood’ and ‘Rapidly progressive’.

The Structure of the Human Phenotype Ontology -- The ontologies are structured as directed acyclic graphs (DAG), which are similar to hierarchies but differ in that a more specialized term (child) can be related to more than one less specialized term (parent).

Cycles (cyclic paths in the graph) are Not allowed. The relationship of the terms of the HPO to one another is displayed in the DAG.

For instance, the term Aplasia/Hypoplasia of metatarsal bones is a child of both Aplasia/Hypoplasia involving bones of the feet and Abnormalities of the metatarsal bones.

The ability to encode multiple parents in a DAG adds to the flexibility and descriptiveness of the ontology.

For instance, it is possible to search for all terms involving Aplasia/Hypoplasia of the skeleton as well as to search for all terms involving abnormalities of the foot.

This would Not be possible with a simple hierarchical system.

Currently, all relationships in the HPO are 'is_a' relationships, i.e. a simple class-subclass relationship.

For instance, Abnormality of the feet 'is_a' Abnormality of the lower limbs.

The relationships are transitive, meaning that they are ‘inherited up’ all paths to the root.

For instance, Abnormality of the lower limbs 'is_a' Abnormality of the extremities, and thus Abnormality of the feet also 'is' Abnormality of the extremities.

The following advanced HPO tools are provided --

1) PhenExplorer - An AJAX-application used to explore the HPO by visualizing the HPO terms to which Mendelian diseases are annotated or by finding all diseases in the OMIM annotated to any one of the > 8,000 HPO terms.

2) HPO Tree Browser - Used to view the HPO in the form of a tree. It shows disease genes, if applicable.

3) Gene2HPO - With this tool you can enter a ‘gene name’ (or a list of gene names, separated by spaces) and search for all related phenotypic features (features found in diseases associated with mutations in the genes).

System Requirements

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Manufacturer Web Site Human Phenotype Ontology

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G6G Abstract Number 20290

G6G Manufacturer Number 100505