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geneontology

Gene Ontology Consortium. http://www.geneontology.org. DictyBase. The Pathogen Group. Schizosaccharomyces pombe Genome Sequencing Project. Extending to the GO model OBO open biology ontologies http://obo.sf.net/

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geneontology

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

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

  3. obo.sf.net obo

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

  5. Implicit ontologies within the GO: • cysteine biosynthesis (ChEBI) • myoblast fusion (Cell Type Ontology) • hydrogen ion transporter activity (ChEBI) • snoRNA catabolism (Sequence Ontology) • wing disc pattern formation (Drosophila anatomy) • epidermal cell differentiation (Cell Type Ontology) • regulation of flower development (Plant anatomy) • interleukin-18 receptor complex (not yet in OBO) • B-celldifferentiation (Cell Type Ontology)

  6. Integrating ontologies CL GO blood cell cell differentiation lymphocyte differentiation lymphocyte B-cell activation B-cell is_a B-cell differentiation

  7. [ Term ] id: GO:0030183 name: B-cell differentiation is_a: GO:0042113 ! B-cell activation is_a: GO:0030098 ! lymphocyte differentiation intersection_of: is_a GO:0030154 ! cell differentiation intersection_of: has_participant CL:0000236 ! B-cell Augmented GO [ Term ] id: CL:0000236 name: B-cell is_a: CL:0000542 ! lymphocyte develops_from: CL:0000231 ! B-lymphoblast Current CL

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

  9. entity describes attribute has value

  10. Allele: cora[5]; Fbal:0089377 Reference: Fbrf:0105869; PUBMED:9843584 Entity: dorsal closure; Attribute: completion; Value: incomplete Entity: cuticle; Attribute: relative_thickness; Value: thin Entity: cuticle; Attribute: structure; Value: necrotic Entity: trachea; Attribute: inflation; Value: abnormal Entity: septate junction; Attribute: structure; Value: abnormal Entity: salivary gland; Attribute: permeability; Value: impermeable Entity: epithelium; Attribute: permeability; Value: impermeable

  11. gene: SHH; OMIM:600725 syndrome: holoprosencephaly 3; OMIM:142945 disease: Holoprosencephaly ; DOID:0000257 Reference: OMIM:142945 Reference: www.ninds.nih.gov/disorders/holoprosencephaly/holoprosencephaly.htm Entity: prosencephalon development ; Attribute: process; Value: arrested Entity: brain ; Attribute: relative_size ; Value: small Entity: brain ventricle ; Attribute: number ; Value: single Entity: skull ; Attribute: morphology ; Value: abnormal Entity: midface ; Attribute: structure ; Value: hypoplastic Entity: eye ; Attribute: morphology ; Value: abnormal Entity: eye ; Attribute: number ; Value: single Entity: eye ; Attribute: placement ; Value: mislocalized Entity: nose ; Attribute: morphology ; Value: abnormal Entity: nostril ; Attribute: number ; Value: single Entity: upper lip ; Attribute: morphology ; Value: cleft Entity: kidney ; Attribute: relative_size ; Value: hypertrophied

  12. Development of phenotype and associated ontologies. Retrofit FlyBase phenotype curation with PO. Curation of OMIM diseases with PO. Emphasis on genes with clear fly/human homologs.

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