The Gene Ontology Project

DNA

gene gene gene gene gene

mRNA

protein

http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/html/fnmol-01-007/images/article/image_n/fnmol-01-007-g001.gif

substrate + O2 = CO2 +H20 product

http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

Gene product:• What does it do?• Where does it do it?• What is the bigger picture?

Clark et al., 2005

part_of

is_a

Clark et al., 2005

part_of

is_a

Whole genome analysis(J. D. Munkvold et al., 2004)

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabolismImmune response

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

See which processes are upregulated or downregulated.

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

Current metrics

• 3 ontologies– Biological process– Molecular function– Cellular component

• 26,933 terms• 5 relationship types• 47,000+ relationships• 40,000,000+ annotations• 88,193 species.

Future plans

• Cross products

• Function-process links

Cross products: Identify ontologies within ontologies – make computable

Intersection tags / cross products

[Term]

id: GO:0010064 ! embryonic shoot morphogenesis

intersection_of: GO:0010016 ! shoot morphogenesis

intersection_of: part_of GO:0009790 ! embryonic development

[Term]

id: GO:0010101 ! post-embryonic root morphogenesis

intersection_of: GO:0010015 ! root morphogenesis

intersection_of: part_of GO:0009791 ! post-embryonic development

Cross products (xp) in progress

• XPs being set up amongst GO ontologies.

• Also with:

cell type ontology,

uberon (anatomy) ontology,

ChEBI (chemical) ontology.

• 170+ new relationship types planned.

Link out to other ontologies:

• Open Biomedical Ontologies– 54 compatible ontologies– 26 other nearly compatible ontologies

http://www.obofoundry.org/

Function-process links

http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP ->

UDP-D-glucose + diphosphate

glucose metabolic process

UDP-glucosemetabolicprocess galactose

metabolic process

biosyntheticprocess

colanic acidbiosyntheticprocess

responseto desiccation

carbohydrate catabolic process

Function

Processhp hp

hphp hp

hp hp

hp = has_part

Lysine biosynthesis pathways

lysinebiosynthesis

lysinebiosynthesis1

lysinebiosynthesis3

lysinebiosynthesis2

lysinebiosynthesis4

lysinebiosynthesis5

lysinebiosynthesis6

Function

Process

is_a

is_ais_a is_a is_a

is_a

lysinebiosynthesis 7?

is_a

Process

Function

Lysine Biosynthesis

Process B Process C

Shared function?

= has_part

Non-shared function

new GO term

existing GO term

Process

Function

Lysine Biosynthesis

Process B Process CRelationship explosion

(or Editorial office explosion)

Tools

OBO-Edit: Ontology Editor Tool

Reasoner finds missing and redundant relationships.

2006 Consortium Meeting,

St. Croix,

U.S. Virgin Islands, March 30 - April 3, 2006

http://www.geneontology.org

Reactome

E. Coli hub

Particular thanks to:

Chris Mungall - OBOL,

Rule Based Reasoner

Cross product system

Function process link plan – The electron transport working group

OBO-Edit:

John Day-Richter,

Nomi Harris,

Amina Abdulla: