Gene Ontology Consortium The Pathogen Group Schizosaccharomyces pombe Genome Sequencing Project DictyBase.

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Presentation transcript:

Gene Ontology Consortium The Pathogen Group Schizosaccharomyces pombe Genome Sequencing Project DictyBase

Extending to the GO model OBO open biology ontologies aka - extended go - (ego)

obo obo.sf.net

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

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-cell differentiation (Cell Type Ontology) Implicit ontologies within the GO:

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

[ Term ] id: GO: name: B-cell differentiation is_a: GO: ! B-cell activation is_a: GO: ! lymphocyte differentiation intersection_of: is_a GO: ! cell differentiation intersection_of: has_participant CL: ! B-cell [ Term ] id: CL: name: B-cell is_a: CL: ! lymphocyte develops_from: CL: ! B-lymphoblast Augmented GO Current CL

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

value entity describes attribute has

Allele: cora[5]; Fbal: Reference: Fbrf: ; PUBMED: 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

gene: SHH; OMIM: syndrome: holoprosencephaly 3; OMIM: disease: Holoprosencephaly ; DOID: Reference: OMIM: Reference: 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

1.Development of phenotype and associated ontologies. 2.Retrofit FlyBase phenotype curation with PO. 3.Curation of OMIM diseases with PO. 4.Emphasis on genes with clear fly/human homologs.