Saturday, August 29, 2009

Australia, taxonomy, and integration

I recently traveled to Canberra, Australia thanks to an invite from John La Salle at CSIRO. John is one of the driving forces behind the Atlas of Living Australia, a initiative recently funded on the scale of EOL. While there I attended a couple of short workshops on phenomics and biosecurity and presented talks on the HAO. One recurring topic was how ontologies could be used to speed taxonomy. There are obvious applications, for instance our text markup proofing tool, but clearly a lot more is possible.

La Salle, for example, is pushing the idea of automated character recognition (PDF). Imagine an anatomy ontology, such as the HAO, that has associated with it a large number of annotations on images - e.g., that light micrograph of an ant head has polygons and/or point markers superimposed over it that indicate which structures are the compound eyes, ocelli, face, antennae, etc. These core data could act as the basis for algorithmic recognition on images of other ants. While this functionality is largely science fiction at the moment, it's possible that the technology will be folded into the taxonomic workflow within my lifetime. We will spend a lot of time in the next three years thinking about this and other ways the HAO can be used to address the taxonomic impediment.

Integrating the HAO with taxonomy maybe be somewhat abstract, but by the virtue of being an OBO format file available to the others the HAO is already being integrated into the ontological world (semantic web?). Richard Cole wrote to us to point out that the HAO is now visible via the Ontology Lookup Service. This service provides a nice graph to visualize and navigate the ontology. If you have other useful or cool applications that use OBO ontologies let us know and we'll point them.

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