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. 2016 May 18:7:28.
doi: 10.1186/s13326-016-0074-0. eCollection 2016.

The cellular microscopy phenotype ontology

Simon Jupp  1 , James Malone  1 , Tony Burdett  1 , Jean-Karim Heriche  2 , Eleanor Williams  3 , Jan Ellenberg  2 , Helen Parkinson  1 , Gabriella Rustici  1
Affiliations

The cellular microscopy phenotype ontology

Simon Jupp et al. J Biomed Semantics. .

Abstract

Background: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues.

Description: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process.

Conclusion: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability.

Keywords: Cellular phenotype; Imaging; OWL; Ontology.

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Figures

Fig. 1
Fig. 1
Visualisation of the top-level terms in the CMPO phenotype ontology showing cell process, single cell, cellular component and molecular component phenotypes
Fig. 2
Fig. 2
Screenshot of the Image Data Repository showing image meta-data that include phenotype annotation to CMPO term “decreased duration of mitotic prophase” [CMPO:0000329]
See this image and copyright information in PMC

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