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Extending to the GO model OBO open biology ontologies

Extending to the GO model OBO open biology ontologies http://obo.sf.net/ aka - extended go - (ego). obo.sf.net. obo. The aims of SO. Develop a shared set of terms and concepts to annotate biological sequences .

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Extending to the GO model OBO open biology ontologies

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  1. Extending to the GO model OBO open biology ontologies http://obo.sf.net/ aka - extended go - (ego)

  2. obo.sf.net obo

  3. The aims of SO • Develop a shared set of terms and concepts to annotate biological sequences. • Apply these in our separate projects to provide consistent query capabilities between them. • Provide a software resource to assist in the application and distribution of SO.

  4. What is a pseudogene? • Human • Sequence similar to known protein but contains frameshift(s) and/or stop codons which disrupts the ORF. • Neisseria • A gene that is inactive - but may be activated by translocation (e.g. by gene conversion) to a new chromosome site. • - note such a gene would be called a “cassette” in yeast.

  5. Give me all the dicistronic genes • Define a dicistronic gene in terms of the cardinality of the transcript to open-reading-frame relationship and the spatial arrangement of open-reading frames.

  6. ISA—927 relationships PARTOF—186 relationships holonym meronym

  7. Classical Extensional Mereology • The formal properties of parts: • If A is a proper part of B then B is not a part of A (nothing is a proper part of itself) • If A is a part of B and B is a part of C then A is a part of C • Because of these rules, we can apply some functions to parts…

  8. Extensional Mereology (EM) : a formal theory of parts

  9. Exon distribution to transcripts Drosophila chromosome 4.

  10. Anatomy Ontologies For the representation of phenotypic and expression data. Now available for: Drosophila, Mus, C. elegans, Arabidopsis, Ozyra ….

  11. The need for a (bio)chemical ontology. • CAS - commercial & expensive. • LIGAND - no internal structure. • MESH - semantically weak, very biased • towards pharmaceutical agents. • ChEBI - in development at EBI - 1st release • was June 2004.

  12. Tissue, cell & pathology ontologies. Medical ontologies - e.g. SNOMED - (a) commercial. (b) designed not for research, but for billing.

  13. The next challenge A syntax and semantics for the description of phenotypic data.

  14. entity describes attribute has value

  15. Thank yous • Berkeley • Chris Mungall, John Richter, Brad Marshall • Insightful biologists • Midori Harris, David Hill, Bernard de Bono • My Co-founders • Suzanna Lewis, Judith Blake, and Mike Cherry • The GO Editorial Team at the EBI • Midori Harris, Jane Lomax, Amelia Ireland & Jennifer Clark • SO: Karen Eilbeck, Mark Yandel • And many, many more…

  16. Gene Ontology Consortium http://www.geneontology.org DictyBase The Pathogen Group Schizosaccharomyces pombe Genome Sequencing Project

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