Extending to the GO model

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

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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.

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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.

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• ISA927 relationships

• PARTOF186 relationships

holonym
meronym
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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

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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 (x?y) 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 (xy) The largest portion of x which has no part in common with y.
Binary Sum (xy) The set consisting of individuals x and y
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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 gt 1 but lt all 74 (16)
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Anatomy Ontologies For the
representation of phenotypic and expression
data. Now available for Drosophila, Mus, C.
elegans, Arabidopsis, Ozyra .
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• 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.

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Tissue, cell pathology ontologies. Medical
ontologies - e.g. SNOMED - (a) commercial. (b)
designed not for research, but for
billing.
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The next challenge A
syntax and semantics for the description of
phenotypic data.
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entity
describes
attribute
has
value
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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

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