List Of Standards And Ontologies In Cellular Image Data Sets
Year: 2015
Type: report
Abstract: The WP6 use case of BioMedBridges addresses interoperability of large-scale image data sets, which is required for reusing and analysing data sets generated by different sources. The following aspects of image data sets significantly influence their interoperability: File formats Accessibility of the data Image annotation Currently, over 100 different file formats are in use by the cellular biology community. This high diversity contributes to the low interoperability of the data coming from different sources. However, significant efforts have been made recently by the cell biology community towards the wider adoption of two file format standards, OME-TIFF for individual images and HDF5 for large and complex datasets. The adoption of standard image file formats will facilitate interoperability and reuse of image data. The high volume of cell microscopy data generated by the cell biology community is rarely shared in a visible and publicly accessible way and is therefore not easily accessible to external researchers. Euro-BioImaging, together with ELIXIR, is planning to provide access to standardised, annotated image data repositories supported by repositories of interoperable and quality-controlled tools for image data analysis. Finally, consistent annotation of cellular image data sets is required for their interoperability. Although numerous ontologies for cell biology are available, none of them covers comprehensively cellular microscopy phenotype. Therefore, image data sets are normally annotated using free text or a diverse set of ontologies. To bridge the gap between existing ontologies, WP6 partners are currently developing the cellular microscopy phenotype ontology (CMPO).
DOI: 10.5281/zenodo.14124
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: green
Funder: European Commission
OpenAlex ID: W2231423640