Oxford 0410 2

Slide1: 

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

Slide2: 

Slide3: 

obo: 

obo obo.sf.net

Slide5: 

The aims of SO: 

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.

What is a pseudogene?: 

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: 

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.

Slide9: 

ISA—927 relationships PARTOF—186 relationships holonym meronym

Classical Extensional Mereology: 

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…

Slide11: 

Extensional Mereology (EM) : a formal theory of parts

Slide12: 

Exon distribution to transcripts Drosophila chromosome 4.

Slide13: 

Slide14: 

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

Slide15: 

Slide16: 

Slide17: 

Slide18: 

Slide19: 

Slide20: 

Slide21: 

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

Slide22: 

Slide23: 

Slide24: 

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

Slide25: 

Slide26: 

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

Slide27: 

value entity describes attribute has

Thank yous: 

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 andamp; Jennifer Clark SO: Karen Eilbeck, Mark Yandel And many, many more…

Slide29: