title: 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.
authors.affiliation: Berlin Brandenburg Center for Regenerative Medicine, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Max Delbrück Center for Molecular Medicine, Computational Biology and Data Mining, Berlin 13125, Germany, Humboldt Universität zu Berlin, Institute for Computer Science, Berlin 10099, Germany and Seoul National University, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul 151-742, Republic of Korea.
authors.forename: Harald
authors.initials: H
authors.lastname: Stachelscheid
authors.forename: Stefanie
authors.initials: S
authors.lastname: Seltmann
authors.forename: Fritz
authors.initials: F
authors.lastname: Lekschas
authors.forename: Jean-Fred
authors.initials: JF
authors.lastname: Fontaine
authors.forename: Nancy
authors.initials: N
authors.lastname: Mah
authors.forename: Mariana
authors.initials: M
authors.lastname: Neves
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.forename: Ulf
authors.initials: U
authors.lastname: Leser
authors.forename: Andreas
authors.initials: A
authors.lastname: Kurtz
mesh_terms: D000818:Animals; D002460:Cell Line; D002468:Cell Physiological Phenomena; D002477:Cells / Q000166:cytology / Q000378:metabolism*; D022082:Cellular Structures / Q000648:ultrastructure; D057225:Data Mining; D016208:Databases, Factual; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D007668:Kidney / Q000166:cytology; D008099:Liver / Q000166:cytology; D011506:Proteins / Q000378:metabolism; D012313:RNA / Q000378:metabolism
chemical_list: D011506:Proteins; D012313:RNA