title: RegenBase: a knowledge base of spinal cord injury biology for translational research.
abstract: Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org.
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305.
authors.forename: Alison
authors.initials: A
authors.lastname: Callahan
authors.affiliation: Department of Computer Science, University of Miami, Coral Gables, FL 33146.
authors.forename: Saminda W
authors.initials: SW
authors.lastname: Abeyruwan
authors.affiliation: Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136.
authors.forename: Hassan
authors.initials: H
authors.lastname: Al-Ali
authors.affiliation: Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136.
authors.forename: Kunie
authors.initials: K
authors.lastname: Sakurai
authors.affiliation: Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, San Francisco; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94143.
authors.forename: Adam R
authors.initials: AR
authors.lastname: Ferguson
authors.affiliation: Center for Brain and Spinal Cord Repair and the Department of Neuroscience, The Ohio State University, Columbus, OH 43210.
authors.forename: Phillip G
authors.initials: PG
authors.lastname: Popovich
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305.
authors.forename: Nigam H
authors.initials: NH
authors.lastname: Shah
authors.affiliation: Department of Computer Science, University of Miami, Coral Gables, FL 33146.
authors.forename: Ubbo
authors.initials: U
authors.lastname: Visser
authors.affiliation: Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136 Center for Computational Science, University of Miami, Coral Gables, FL 33146 Department of Cellular and Molecular Pharmacology, University of Miami School of Medicine, Miami, FL 33136, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Bixby
authors.affiliation: Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136 Center for Computational Science, University of Miami, Coral Gables, FL 33146 vlemmon@miami.edu.
authors.forename: Vance P
authors.initials: VP
authors.lastname: Lemmon
mesh_terms: D000818:Animals; D016208:Databases, Factual; D004195:Disease Models, Animal; D006801:Humans; D051188:Knowledge Bases; D051379:Mice; D051381:Rats; D013119:Spinal Cord Injuries; D057170:Translational Research, Biomedical