http://www.geneontology.orgGene Ontology Consortium

The Pathogen Group

Schizosaccharomyces pombeGenome Sequencing Project

DictyBaseQuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.

Extending to the GO model

OBO

open biology ontologies

http://obo.sf.net/

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

lymphocytedifferentiati

onlymphocyte

B-cell

GO CL

is_a

cell differentiation bloodcell

B-cellactivatio

n

Integrating ontologies

[ Term ]id: GO:0030183name: B-cell differentiationis_a: GO:0042113 ! B-cell activationis_a: GO:0030098 ! lymphocyte differentiationintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000236 ! B-cell

[ Term ]id: CL:0000236name: B-cellis_a: CL:0000542 ! lymphocytedevelops_from: CL:0000231 ! B-lymphoblast

AugmentedGO

CurrentCL

The next challenge

A syntax and semantics for the descriptionof phenotypic data.

value

entitydescribes

attributehas

Allele: cora[5]; Fbal:0089377Reference: Fbrf:0105869; PUBMED:9843584Entity: dorsal closure; Attribute: completion; Value: incompleteEntity: cuticle; Attribute: relative_thickness; Value: thinEntity: cuticle; Attribute: structure; Value: necroticEntity: trachea; Attribute: inflation; Value: abnormalEntity: septate junction; Attribute: structure; Value: abnormalEntity: salivary gland; Attribute: permeability; Value: impermeableEntity: epithelium; Attribute: permeability; Value: impermeable

gene: SHH; OMIM:600725syndrome: holoprosencephaly 3; OMIM:142945disease: Holoprosencephaly ; DOID:0000257Reference: OMIM:142945Reference: www.ninds.nih.gov/disorders/holoprosencephaly/holoprosencephaly.htmEntity: prosencephalon development ; Attribute: process; Value: arrestedEntity: brain ; Attribute: relative_size ; Value: smallEntity: brain ventricle ; Attribute: number ; Value: singleEntity: skull ; Attribute: morphology ; Value: abnormalEntity: midface ; Attribute: structure ; Value: hypoplasticEntity: eye ; Attribute: morphology ; Value: abnormalEntity: eye ; Attribute: number ; Value: singleEntity: eye ; Attribute: placement ; Value: mislocalizedEntity: nose ; Attribute: morphology ; Value: abnormalEntity: nostril ; Attribute: number ; Value: singleEntity: upper lip ; Attribute: morphology ; Value: cleftEntity: 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.