Jupp, S;
Malone, J;
Burdett, T;
Heriche, J-K;
Williams, E;
Ellenberg, J;
Parkinson, H;
(2016)
The cellular microscopy phenotype ontology.
Journal of Biomedical Semantics
, 7
, Article 28. 10.1186/s13326-016-0074-0.
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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.
| Type: | Article |
|---|---|
| Title: | The cellular microscopy phenotype ontology |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1186/s13326-016-0074-0 |
| Publisher version: | https://doi.org/10.1186/s13326-016-0074-0 |
| Language: | English |
| Additional information: | © 2016 Jupp et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Mathematical & Computational Biology, Ontology, OWL, Cellular phenotype, Imaging, Genome-Wide Rnai, Systems Microscopy, Database, Biology, Tool |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10036025 |
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