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Published January 21, 2015 | Version v1
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Mapping of standards and ontologies between the different image reference data sets

  • 1. EMBL-European Bioinformatics Institute
  • 2. European Molecular Biology Laboratory
  • 3. Helmholtz Institute Munich
  • 4. FIMM

Description

The imaging use case of BioMedBridges addresses interoperability of large-scale image data sets, which is required for reusing and comparatively analyzing data sets generated by different sources. 

One of the most commonly done types of analysis of image data is annotation of cellular phenotype. However, phenotypic data associated with image datasets is often annotated using free-text which can vary widely from researcher to researcher for the same phenotype, or by using ontologies that are specific for particular species or level of annotation, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues.

To harmonize the annotation of cellular phenotypes, WP6 partners have developed the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing general 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 is made to be used by any researcher generating phenotypic data who are annotating cellular phenotypes associated with their imaging data.

Preliminary testing of CMPO for the annotation of imaging datasets derived from different biological domains (cell lines, mouse and human tissues) is showing that CMPO is suitable to annotate cellular phenotypes observed in such images, consequently making the data interoperable.

Files

BioMedBridges_D6_4_Mapping_of_standard_and_ontologies.pdf

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Additional details

Funding

BIOMEDBRIDGES – Building data bridges between biological and medical infrastructures in Europe 284209
European Commission