Abstract
HSC-Explorer (http://mips.helmholtz-muenchen.de/HSC/) is a publicly available, integrative database containing detailed information about the early steps of hematopoiesis. The resource aims at providing fast and easy access to relevant information, in particular to the complex network of interacting cell types and molecules, from the wealth of publications in the field through visualization interfaces. It provides structured information on more than 7000 experimentally validated interactions between molecules, bioprocesses and environmental factors. Information is manually derived by critical reading of the scientific literature from expert annotators. Hematopoiesis-relevant interactions are accompanied with context information such as model organisms and experimental methods for enabling assessment of reliability and relevance of experimental results. Usage of established vocabularies facilitates downstream bioinformatics applications and to convert the results into complex networks. Several predefined datasets (Selected topics) offer insights into stem cell behavior, the stem cell niche and signaling processes supporting hematopoietic stem cell maintenance. HSC-Explorer provides a versatile web-based resource for scientists entering the field of hematopoiesis enabling users to inspect the associated biological processes through interactive graphical presentation.
Highlights
The term ‘‘Hematopoiesis’’ describes the life-long regeneration and repair of the blood system
All blood cells are generated from multipotent hematopoietic stem cells (HSCs) which are the only cell type capable of long-term self-renewal
Curation of Information from hematopoietic literature The complete content of the database is generated by biocurators who manually extract hematopoiesis-specific and experimentally verified information from the scientific literature
Summary
The term ‘‘Hematopoiesis’’ describes the life-long regeneration and repair of the blood system. The use of such terms is not consistent throughout the literature This inconsistency together with the intrinsic heterogeneity of the HSC compartment [7,8] hampers proper interpretation and direct comparison of results from different publications. For this reason a comprehensive understanding of the current knowledge in the field requires the collection of the various experimental results, within a unified resource. We present HSC-Explorer, a publicly available, manually curated, integrative database collecting literature-derived knowledge about the different hematopoietic stem cell subpopulations and their behavior in repopulation activity, self-renewal and quiescence and how these processes are regulated by intrinsic and extrinsic factors. Multiple search options and an interactive graphical tool enable information retrieval of the manifold interrelations between factors and processes and their presentation as informative network structures
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