gene ontology consortium the pathogen group schizosaccharomyces pombe genome sequencing project...
DESCRIPTION
Gene Ontology Consortium The Pathogen Group Schizosaccharomyces pombe Genome Sequencing Project DictyBaseTRANSCRIPT
http://www.geneontology.orgGene Ontology Consortium
The Pathogen Group
Schizosaccharomyces pombeGenome Sequencing Project
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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.