This page hosts a link to a copy of the Crystallization Data Exchange (XDX) OWL ontology.

OWL Ontology: Now moved to GitHub (as of 29/Jan/2015).

This ontology is currently under development at CSIRO in Australia. If you wish to participate or have any suggestions or comments, please contact us at:

Email: admin@xdx-ontology.info

Background

Protein crystallisation is a difficult problem, often requiring hundreds to thousands of experiments over weeks, months or even years to be carried out before a suitable crystal can be produced for further analysis.

Our goal is to integrate experimental data from crystallisation labs and online holdings such as the RCSB Protein Data Bank (PDB) and the Biological Macromolecule Crystallization Database (BMCD) using the Semantic Web technologies OWL and RDF under a common semantic framework using the nomenclature captured in the XDX OWL ontology and associated vocabularies. In doing so, we aim to construct an integrated resource for data mining the experimental data to look for conditions which are most (or least) amenable for crystallisation. Current attempts have not incorporated the vast amount of negative experimental condition data (those which did not produce a crystal as an outcome), but which are essential for a rigorous statistical analysis of experiments against their outcomes.

Note that while we will not prescribe URIs for the identity of objects in experiments such as chemical compounds (where ChEBI or PubChem RDF identifiers are preferable), we may do so for objects such as particular experimental apparatuses and setup methods, such as Hanging/Sitting Drop Vapour Diffusion, for which no current authoritative URIs are known. We welcome any suggestions.

Relevant Publications

Newman, J., Bolton, E.E., Mller-Dieckmann, J., Fazio, V.J., Gallagher, D.T., Lovell, D., Luft, J.R., Peat, T.S., Ratcliffe, D., Sayle, R.A., Snell, E.H., Taylor, K., Vallotton, P., Velanker, S., von Delft, F.: On the need for an international effort to capture, share and use crystallization screening data. Acta Crystallographica Section F Structural Biology and Crystallization Communications 68(3), 253–258 (Feb 2012).

Einspahr, H., Weiss, M.S.: Call for a crystallization ontology. Acta Crystallographica Section F Structural Biology and Crystallization Communications 68(3), 252–252 (Feb 2012).

Links