Toward an ontological database for subcellular neuroanatomy

  • Authors:

  • Amarnath Gupta;Stephen D. Larson;Christopher Condit;Sandeep Gupta;Lisa Fong;Li Chen;Maryann E. Martone

  • Affiliations:

  • University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA;University of California San Diego, La Jolla, CA

  • Venue:
  • ER'07 Proceedings of the 2007 conference on Advances in conceptual modeling: foundations and applications
  • Year:
  • 2007

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Abstract

We present the semantic data model for an ontological database for subcellular anatomy for Neurosciences. The data model builds upon the foundations of OWL and the Basic Formal Ontology, but extends them to include novel constructs that address several unresolved challenges encountered by biologists in using ontological models in their databases. The model addresses the interplay between models of space and objects located in the space, objects that are defined by constrained spatial arrangements of other objects, the interactions among multiple transitive relationships over the same set of concepts and so on. We propose the notion of parametric relationships to denote different multiple ways of parcellating the same space. We also introduce the notion of phantom instances to address the mismatches between the ontological properties of a conceptual object and the actual recorded instance of that object in cases where the observed object is partially visible.