CellFinder: a cell data repository

Abstract

CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder’s data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder’s web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians.

Evaluating Cell Identity from Transcription Profiles

“…Transcriptome data was collected from published 13 of 24 Figure 1A and a complete list of all samples is given in Supplementary Data S1. Samples were manually annotated for their tissue origin and cell types using ontology terms (Malone et al, 2010;Stachelscheid et al, 2014). Raw microarray data were obtained from the public repositories Gene Expression Omnibus and ArrayExpress (Barrett et al, 2009;Rustici et al, 2013).…”

Therapeutic Complement Targeting in ANCA-Associated Vasculitides and Thrombotic Microangiopathy

“…Such depth of characterization is also necessary to unambiguously classify hiPSC-derived renal cell types by comparing these cells to their native equivalents. Technological tools are now available to characterize cells on the single-cell level and to analyze the associated data [34]. At the BCRT, we have developed a registry of cell type-associated data as a first step to characterize most or all distinct cell types of the kidney and other organs (Fig.…”

Regulatory Insight into the European Human Pluripotent Stem Cell Registry

“…This includes an online registration tool and expanded options for registration of ethical, scientifi c, and quality data as well as uploading of documents such as protocols, and ethical and regulatory documentation. The provision of easy browsing of cell -and project -related information for registered cell lines in hESCreg also requires the development of new technical solutions such as semantic search algorithms and ontology -based data organization [11].…”