CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses

Abstract

CELLPEDIA is a repository database for current knowledge about human cells. It contains various types of information, such as cell morphologies, gene expression and literature references. The major role of CELLPEDIA is to provide a digital dictionary of human cells for the biomedical field, including support for the characterization of artificially generated cells in regenerative medicine. CELLPEDIA features (i) its own cell classification scheme, in which whole human cells are classified by their physical locations in addition to conventional taxonomy; and (ii) cell differentiation pathways compiled from biomedical textbooks and journal papers. Currently, human differentiated cells and stem cells are classified into 2260 and 66 cell taxonomy keys, respectively, from which 934 parent–child relationships reported in cell differentiation or transdifferentiation pathways are retrievable. As far as we know, this is the first attempt to develop a digital cell bank to function as a public resource for the accumulation of current knowledge about human cells. The CELLPEDIA homepage is freely accessible except for the data submission pages that require authentication (please send a password request to cell-info@cbrc.jp).Database URL: http://cellpedia.cbrc.jp/

CellFinder's Molecular Database and its Application to Stem Cell Research

“…Like CellFinder, contemporary web resources, such as SHOGoiN/CELLPEDIA [10] and Stemformatics [11], also compile cell-based '-omics' data from public repositories, but only the former associates its data to ontology terms. In this communication, we describe the compilation of transcriptome data from microarrays, with a focus on pluripotent stem cells and engineered or otherwise derived cell types.…”

CellFinder: a cell data repository

“…Although expression profiles complement and partially replaced the classical descriptors (4,6), they are not sufficient to fully define the phenotype of a cell; further cytological, morphological and histological images are still of high importance for describing and distinguishing cells in biology and medicine (43). Accordingly, CellFinder comprises gene and protein expression data as well as image data, both of which are integrated by the ontology-based data model (24).…”

“…The need for a fully comprehensive cell type catalog and definition of classification standards is emphasized by different numbers of human cell types provided by CellFinder (1058) versus the 2260 suggested by CELLPEDIA by a combination of conventional taxonomy with physical mappings (4). To the best of our knowledge, our comprehensive and integrated view on cells is a novel and important contribution to the biomedical sciences.…”

LifeMap Discovery™: The Embryonic Development, Stem Cells, and Regenerative Medicine Research Portal

“…In the stem cell field, very few publicly available databases currently exist; each of the existing databases targets certain elements of interest to stem cell research such as expression, regulation [3], [4] [5] or attempted computational classification [4]. However, currently, no resource provides a comprehensive set of information and supporting data needed to study and develop stem cell applications.…”