RKB: a SW knowledge base for RNA (ISMB Bio-Ont SIG 2009)
Michael Dumontier et al.
Wants to capture the structural features and interactions of RNA. Capture types and their relations, represent dynamic / context-specific knowledge, populate the KB with PDB structural data and MC-Annotate interactions, and answer questions about RNA structure. Looked at textbooks, review articles, book chapters, expert knowledge. Their upper-level ontology (ULO) was NULO, based on BFO/RO.
Contextual modelling of nucleic acids: base stacking varies in different NMR etc models. Then he described the Leontis-Westhof Nomenclature, where you describe the edges of the base as participating in the reaction. So a more sophisticated nomenclature was developed that was based on this called LW+ Nomenclature, where they divvied up the edges into a set of faces.
They want to capture information about residues, edges/faces, cis/trans nucleotide orientations, and across parallel/antiparallel strands. Base stacking involves inter-nucleobase interactions that involve London forces. Wanted to capture both numbers and a description of what is going on. They’ve used two roles: FacingAwayRole and FacingTowardsRole. There is both an endo and exo role for sugar puckering. Situational modeling assures that objects are represented by a single entity throught their lifetime.
RKB is popoulated with PDB and MC-Annotate and it is all represented in RDF. The population involved 3 steps: assigningnames, asserting class membership, and ?. So they can then ask the database things using DL queries. RKB is also accessible via SPARQL.
They’re now working with the RNA Ontology Consortium. They want to publish as part of the Bio2RDF netowkr, and extend the structure description with backbone angles.
NULO: there is a logic mapping bewteen NULO and BFO. They’ve relaxed restrictions where it is unclear what BFO’s stance is. It was unclear if you made certain statements you would still fit in with the idea in BFO.
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