The cellular microscopy phenotype ontology

Simon Jupp; James Malone; Tony Burdett; Jean-Karim Heriche; Eleanor Williams; Jan Ellenberg; Helen Parkinson; Gabriella Rustici

doi:10.1186/s13326-016-0074-0

The cellular microscopy phenotype ontology

Simon Jupp (Lead / Corresponding author), James Malone, Tony Burdett, Jean-Karim Heriche, Eleanor Williams, Jan Ellenberg, Helen Parkinson, Gabriella Rustici

Research output: Contribution to journal › Article › peer-review

24 Citations (Scopus)

212 Downloads (Pure)

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.

Original language	English
Article number	28
Number of pages	8
Journal	Journal of Biomedical Semantics
Volume	7
DOIs	https://doi.org/10.1186/s13326-016-0074-0
Publication status	Published - 18 May 2016

Keywords

Ontology
OWL
Cellular phenotype
Imaging

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10.1186/s13326-016-0074-0Licence: CC BY

Final Published Version
© 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.
Final published version, 2.23 MBLicence: CC BY

Building a Next Generation Image Repository: Molecular Annotation and Cloud-based Data Processing and Analysis (Joint with EMBL-EBI and University of Cambridge)
Swedlow, J. (Investigator)
Biotechnology and Biological Sciences Research Council
1/01/15 → 30/06/16
Project: Research

Cite this

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title = "The cellular microscopy phenotype ontology",

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AU - Jupp, Simon

AU - Malone, James

AU - Burdett, Tony

AU - Heriche, Jean-Karim

AU - Williams, Eleanor

AU - Ellenberg, Jan

AU - Parkinson, Helen

AU - Rustici, Gabriella

PY - 2016/5/18

Y1 - 2016/5/18

N2 - 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.

AB - 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.

KW - Ontology

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The cellular microscopy phenotype ontology

Abstract

Keywords

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Projects

Building a Next Generation Image Repository: Molecular Annotation and Cloud-based Data Processing and Analysis (Joint with EMBL-EBI and University of Cambridge)

Cite this