This appears to be hypothetical. Julie has written to the author for more information.
Presentation at a conference (ISWC 2005)
Ontologies for Genomes and Genomic Rearrangements Keith Flanagan, Robert Stevens*, Matthew Pocock, Pete Lee and Anil Wipat School of Computing Science, University of Newcastle upon Tyne Department of Computing Science, University of Manchester
We present an ontology for describing genomes, genome comparisons, their evolution and biological function. We believe that this ontology will aid the community in discussing genomic evolution and support the development of novel genome comparison algorithms. We propose an ontology covering seven sub-domains,
- Physical Components. this includes cells, chromosomes and nucleotides.
- Single Sequence. This will usually relate to the whole of or a portion of a chromosome or plasmid.
- Biological Annotation of Single Sequences.
- Pairwise Comparison. These can be used to describe regions of similarity or homology, and also dissimilarity. There are also terms for mutational events, such as point mutations, insertions and deletions.
- Biological Annotation of Pairwise Comparisons. considers the transformations from a ’source’ to a ’target’ sequence. This ontology provides mechanisms to annotate these transformations with biological information. For example, a particular insertion may be an example of a transposable element insertion. Regions of similarity may be annotated with terms such as ’synteny’, ’shared function’, and ’conserved’. This ontology also describes ways that region-based Biological Annotations can be inferred on a ’target’ sequence based upon that present in the ’source’ sequence.
- Evolutionary History. A formal definition of genome evolution, taking into account that different regions of the same genome may have had different evolutionary histories. This includes the idea of a phylogenetic tree, inheritance of genetic material and ancestors. There are terms describing events such as horizontal and vertical transfer, mutations and re-arrangements.
- Biological Annotation of Evolutionary Histories. This provides mechanisms for the interpretation of phylogenetic trees produced using the terms such as paralogue and orthologue. More complex biological annotations can be built upon this layer, such as defining the archetype of a transposon, or pathogenicity island, and tracing the evolution of these archetypes through the different genomes.
We intend this ontology to provide a framework within which genome comparisons can be analysed. It should assist in sharing data between individuals, and also between different software tools. This will enable more sophisticated algorithms to be developed for automating the comparison process.