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Gene Ontology Consortium
http://www.geneontology.org
QuickTi me™ and a
TIFF ( LZW) decompressor
are needed to see thi s pi ctur e.
The Pathogen
Group
Schizosaccharomyces pombe
Genome Sequencing Project
DictyBase
Extending to the GO model
OBO
open biology ontologies
http://obo.sf.net/
aka - extended go - (ego)
obo.sf.net
obo
Anatomy Ontologies
For the representation of
phenotypic and expression data.
Now available for: Drosophila,
Mus, C. elegans, Arabidopsis,
Ozyra ….
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-cell differentiation (Cell Type Ontology)
Integrating ontologies
CL
GO
blood
cell
cell differentiation
lymphocyte
differentiation
lymphocyte
B-cell
activation
B-cell
is_a
B-cell differentiation
[ Term ]
Augmented id: GO:0030183
name: B-cell differentiation
GO
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
Current
CL
[ Term ]
id: CL:0000236
name: B-cell
is_a: CL:0000542
! lymphocyte
develops_from: CL:0000231 ! B-lymphoblast
The next challenge
A syntax and semantics for the description
of phenotypic data.
entity
describes
attribute
has
value
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
gene: SHH; OMIM:600725
syndrome: holoprosencephaly 3; OMIM:142945
disease: Holoprosencephaly ; DOID:0000257
Reference: OMIM:142945
Reference: www.ninds.nih.gov/disorders/holoprosencephaly/holoprosencephaly.
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.
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