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hPSCreg / human Pluripotent Stem Cell registry
A public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection.
CL / Cell Ontology
An OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. CL, since its inception in 2005, has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CL is mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library.
Maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.
CLO / Cell Line Ontology
A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. CLO includes more than 36000 cell lines derived from over 200 in vivo cell types from various organisms. Collaboration among the CLO, Cell Ontology (CL) and the Ontology for Biomedical Investigation (OBI) has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The CLO hierarchical structure makes it easy to browse, query, and perform automated classification.
Allows to search and browse experiments and explore analyses for the Stem Cell Genomics database. StemBase stores gene expression data derived from Affymetrix expression microarrays and Serial Analysis of Gene Expression (SAGE) libraries. Experimental data are organized into groupings of “samples” which represent different conditions in a given experiment. Samples contain a set of “replicates” made using the same sample under the same experimental conditions and associated with one or more “files” containing the raw expression data.
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