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Phenotype Development and Ontologies Integration for Genetic Research

Explore the integration of ontologies like Gene Ontology and DictyBase for representing phenotype and gene data. Focus on disease curation and gene homologs. Retrofit FlyBase and OMIM diseases with Phenotypic Ontologies.

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Phenotype Development and Ontologies Integration for Genetic Research

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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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