RegenBase: A knowledge base of spinal cord injury biology for translational research

Alison Callahan, Saminda W. Abeyruwan, Hassan Al-Ali, Kunie Sakurai, Adam R. Ferguson, Phillip G. Popovich, Nigam H. Shah, Ubbo Visser, John L. Bixby, Vance P. Lemmon

Research output: Contribution to journalArticle

6 Scopus citations

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.

Original languageEnglish (US)
Article numberbaw040
JournalDatabase
Volume2016
DOIs
StatePublished - 2016

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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