Metadata Ontologie

METADATA & ONTOLOGIES

The consortium is committed to making their research data findable, accessible, interoperable and reusable (FAIR). Achieving interoperability implies to follow established standards and use ontologies to describe samples and experiments. We list here resources of interest for single-cell experiments and bioimaging.

Ontologies

Whenever possible, the consortium members use values defined in the HCA ontology. This ontology includes concepts from other relevant ontologies, such as :

  • EFO (Experimental Factor Ontology) which provides information about many experimental variables available in EBI databases, while Eagle-i resource (ERO) is an ontology of research resources such as instruments, protocols, reagents, animal models and biospecimens
  • The Biological Imaging Methods Ontology (fBBi) is an ontology dedicated to the terms used in biomedical research for imaging and visualization methods, and the BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS).
  • Embryonic structure is described in UBERON and EHDAA2 provides a structured controlled vocabulary of stage-specific anatomical structures of the developing human and is linked to HSAPDB, which includes carnegie stages.
  • Different ontologies describe properties and classes at the cell level : the cell ontology (CL) is a general ontology which applies to cell types in animals; and CPO structures the vocabulary related to morphological and physiological phenotypic characteristics of cells, cell components and cellular processes.

Standards and metadata dictionaries

The HuDeCA consortium strives to be compliant with existing standards, such as The Minimum Information About BIobank data Sharing (MIABIS) which aims to standardize data elements used to describe biobanks, research on samples and associated data. When it comes to describing omics experiments at the cellular level, the HCA metadata dictionary was used as a reference. For bioimaging, the OME data model is the main standard used to facilitate the exchange of microscopy data. The OME-TIFF format is an implementation of that model which takes advantage of the rich metadata defined in OME-XML while retaining the pixels in multi-page TIFF format for compatibility with many more applications. 

Related tools

Different services are available to browse ontologies : EMBL-EBI provides an ontology look-up service (OLS); Bioportal also provides access to commonly used biomedical ontologies and to tools for working with them ; and Ontobee is the default linked data server for most OBO Foundry library ontologies (ontologies dedicated to biological sciences).  For standards and data repositories, it can also be useful to check FAIRsharing and re3data

 

HuDeCA metadata

As HuDeCA is a project focusing on Human Development, the metadata values more specifically related to that domain are listed on a dedicated website.  It enables to see, for instance, the correspondances between the different ways of labelling pre-natal stages and to view the main controlled lists implemented in our application and services.

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