Kidney and Urinary Pathway Ontology (KUPO)

, Last updated by jupp, on Thu, 03/24/2011 - 16:51

The latest version of KUPO is available at http://www.e-lico.eu/public/kupo/kupo.owl. The KUPO is being used to annotate data in the Kidney and Urinary Pathway Knowledge Base (KUPKB), a demo of the ontology in use is available at  http://www.e-lico.eu/kupkb. For more information about the KUPO see:

 

  • Simon Jupp, Julie Klein, Joost Schanstra and Robert Stevens. Developing a Kidney and Urinary Pathway Knowledge Base. Bio-ontologies 2010, Boston, USA.

 

 

  • Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, and Katy Wolstencroft. Populous: A tool for populating ontology templates. Semantic Web Applications and Tools for Life Sciences (SWAT4LS). Dec 2010.

 

 

When describing biological samples for investigations and the findings from those investigations, biologists working in kidney and urinary pathways need to be able to describe a broad portion of biology. The initial version of the KUPO reflects this position. We are using ontologies or portions of ontologies that describe:

  • Kidney and urinary anatomy;
  • the cells in those organs and tissues;
  • the gene products in those cells;
  • the functional attributes of those gene products;
  • the celular components of those cells.

We will also wish to describe pathologies and aspects of the investigations on those experiments such as those in transcriptomics and proteomics.

To this end we have chosen to use the following ontologies:

  • the OBO mouse anatomy;
  • the Gene Ontology (molecular function, biological process and cellular compnent);
  • the cell type ontology.

We will also be taking a look at the disease ontology and  the ontology of biomedical investigations (and related efforts).

While taking a portion of the mouse anatomy makes sense -- we want kidney and the rest of the urinary system -- it makes less sense for GO and some of the others. Whilst we want only mammalian pertinent aspects, it is more difficult to limit GO in the same way as we might limit or scope an anatomy. To some extent,  what we want is a mammalian KUP Slim. We also need to extend portions, such as adding cells pertinent to the KUP domain. Such extensions will be submitted to the appropriate ontology efforts. Other extensions will be the insertion of extensions that will promote querying.

Below is a screenshot of the KUP Ontology  in the Protégé-OWL editor developed by the University of Manchester

 

 

A tiny subtree of the 835-concept initial version of the KUP ontology: