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We just heard the news that the recent Plant Ontology Paper is available online from Plant and Cell Physiology: http://pcp.oxfordjournals.org/content/early/2012/12/05/pcp.pcs163.abstract?keytype=ref&ijkey=y8ieoOz5Ec5iIaT
Right now it is just the abstract with a link to the full text accepted proof. But it has been assigned a DOI, in case you would like to cite it.
This paper focuses on the development and redesign of the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
Stay tuned for link to the full test online soon.