Help & Documentation

Parameter ontology annotations

Ontology annotations are listed in IMPReSS for the purpose of high-throughput phenotyping. When a mutation is found to cause a statistically significant increased, decrease or change to a measurement (when compared against the baseline or wildytpe individuals), it can be annotated with the ontology term suggested in the IMPReSS database. This allows data to be searched by Ontology Terms, helping find the role of a gene in the animal’s physiology, helping find mouse models of human diseases and allowing for cross-species comparison of experimental results.

IMPReSS currently supports two forms of ontologies – Single Term and Entity-Quality (EQ) Ontologies. Single term ontologies consist of a single term used to describe an observed phenotype, e.g. Increased Body Weight [MP:0001260]. EQ ontologies are more complex and are composed of one or more Entity ontology terms and one or more Quality ontology terms, e.g. (Entity)Adult Mouse [MA:0002405] – (Quality)Increased Weight [PATO:0000582].

Most single term ontologies used in IMPReSS are from the MP (Mammalian Phenotype) ontology but the database also holds EMAP (Mouse Embryology) and MA (Adult Mouse Gross Anatomy) terms. Single Term ontologies are used in all pipelines in IMPReSS.

For EQ-style ontologies, IMPReSS supports up to three entity terms and up to two quality terms for describing an individual phenotype. Entity Terms include BSPO, CHEBI, CL, ENVO, GO, IMR and MA. Quality Terms currently only contain PATO ontology terms. Most EQ-style ontologies are used in deprecated/historic pipelines in IMPReSS and are not being actively adopted for the IMPC project.

If, for example, a mutation is found to cause increased body weight, then the term INCREASED is used. If a phenotype is observed but it cannot be clearly described as an increase or decrease, it will be termed ABNORMAL. If an ontology term should only be used if the mouse is of one Sex, or for a particular Option value or a defined Increment, the observation will only be annotated with that ontology term if those conditions are met.

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