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. 2016 Apr 7;2016:baw040.
doi: 10.1093/database/baw040. Print 2016.

RegenBase: A Knowledge Base of Spinal Cord Injury Biology for Translational Research

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Free PMC article

RegenBase: A Knowledge Base of Spinal Cord Injury Biology for Translational Research

Alison Callahan et al. Database (Oxford). .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Subset of the new classes added to the RB, showing the human readable label, alternative term and definition for the BBB score class.
Figure 2.
Figure 2.
The generic event representation (a) for primary findings manually curated from the literature including provenance of the primary finding statement. Classes are shown as yellow boxes, individuals/literals as blue rounded boxes and relations between them as labeled arrows. An example event (b) in RegenBase specifies that the small molecule PD98059 was observed to increase BBB score by 4 points. Provenance for this event states that it was created by Vance Lemmon on September 9 2015 and was sourced from an article with PubMed identifier 18180375.
Figure 3.
Figure 3.
Example representation of assay experimental results using BAO, RB and UO. Classes are shown in yellow with their source ontology in brackets and instances are in blue. All relations except ‘label’ (RDFS) and ‘has identifier’ (SIO) are sourced from BAO. Classes are shown as yellow boxes (with the source ontology in brackets), individuals/literals as blue rounded boxes and relations between them as labeled arrows.

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