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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 1. Develop a shared set of terms and concepts to annotate biological sequences. 2. Apply these in our separate projects to provide consistent query capabilities between them. 3. Provide a software resource to assist in the application and distribution of SO. 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. 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. • ISA—927 relationships • PARTOF—186 relationships holonym meronym Classical Extensional Mereology • The formal properties of parts: 1. If A is a proper part of B then B is not a part of A (nothing is a proper part of itself) 2. • 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… Extensional Mereology (EM) : a formal theory of parts EM operation Definition Overlap (x○y) x and y overlap if they have a part in common. Disjoint (xιy) x and y are disjoint if they share no parts in common. Binary Product (x.y) The parts that x and y share in common. Difference (x–y) The largest portion of x which has no part in common with y. Binary Sum (x+y) The set consisting of individuals x and y Exon distribution to transcripts Drosophila chromosome 4. Exon part of single transcript 285 Exon in all transcripts 243 (52%) Exon in one transcript 148 (32%) Exon in > 1 but < all 74 (16%) Anatomy Ontologies For the representation of phenotypic and expression data. Now available for: Drosophila, Mus, C. elegans, Arabidopsis, Ozyra …. 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. Tissue, cell & pathology ontologies. Medical ontologies - e.g. SNOMED (a) commercial. (b) designed not for research, but for billing. The next challenge A syntax and semantics for the description of phenotypic data. entity describes attribute has value 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… Gene Ontology Consortium http://www.geneontology.org Quick Time™ an d a TIFF ( LZW) dec ompre sso r ar e n eed ed to s ee this pic ture . The Pathogen Group Schizosaccharomyces pombe Genome Sequencing Project DictyBase