title: 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.
authors.affiliation: Charité-Universitätsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Seltmann
authors.forename: Harald
authors.initials: H
authors.lastname: Stachelscheid
authors.forename: Alexander
authors.initials: A
authors.lastname: Damaschun
authors.forename: Ludger
authors.initials: L
authors.lastname: Jansen
authors.forename: Fritz
authors.initials: F
authors.lastname: Lekschas
authors.forename: Jean-Fred
authors.initials: JF
authors.lastname: Fontaine
authors.forename: Throng Nghia
authors.initials: TN
authors.lastname: Nguyen-Dobinsky
authors.forename: Ulf
authors.initials: U
authors.lastname: Leser
authors.forename: Andreas
authors.initials: A
authors.lastname: Kurtz
mesh_terms: D002477:Cells / Q000145:classification* / Q000378:metabolism; D022082:Cellular Structures; D053595:Embryonic Stem Cells; D015870:Gene Expression; D006801:Humans; D007668:Kidney / Q000166:cytology; D018875:Vocabulary, Controlled