CELDA -- an ontology for the comprehensive representation of cells in complex systems

Abstract

Background: The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms.

Results: CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org).

Conclusions: CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology.

Figure 1

An overview about the different classes that are used to describe a cell type.

Figure 2

Linking of ontologies in CELDA using BioTop. This diagram shows how high-level classes of CL, CLO, EFO, EHDAA, FMA, GO, MA and UBERON are linked together in CELDA using BioTop. Read from top to bottom, the lines represent rdfs:subclassOf relations.

Figure 3

Domain representation in CELDA. CELDA distinguishes between cells and cell lines. Subclasses of cells describe groups of cells with similar properties like developmental stage, anatomical location, cellular structures or expressed molecules in vitro or in vivo. Cell lines are permanently established cell populations consisting of cells in vitro from exactly one cell type.

Figure 4

How to connect various classes with the label “cell”. Several of the ontologies imported into CELDA contain classes labeled “cell” or “cell type”. The figure shows which of these are stated to be equivalent or connected by means of rdfs: subclassOf relations in CELDA.

Figure 5

An extract from the representation of a ‘parietal epithelial cell’ in the CELDA ontology. Extra classes for a detailed description of these cell types were included, and the ro:develops from relations where added. Furthermore, we linked the cell types to the anatomical entities where they occurred.

Figure 6

An extract of the representation of the human embryonic cell line H1 and the relation to its in vivo counterpart in the CELDA ontology. We added new cell lines like H1 as described in hESCreg when they are not already contained in the CLO.

Figure 7

An extract of the developmental tree of cells that is part of the CELDA - Ontology. Read from top to bottom, the lines represent the ro: develops from relation.