1. Universal descriptions of gene and gene product attributes
Gene Ontology (GO) -
Universal descriptions of gene and gene product attributes
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

2. The Gene Ontology Project
maintain and further develop its controlled vocabulary
annotate genes and gene products
provide tools to facilitate access
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

3. Naming Ambiguity in Bio-Chemical Models
Modelling example: how to name the entities?
ATP or Adenosine-3-phosphate or Adenosinetriphosphate?
Fructose-1,6-bisphosphate or F16P or rather F16BP?
Which database needs what naming convention?
What if different databases have different names for
equal entities?
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

4. What Is an Ontology? Controlled Vocabulary Taxonomy Ontology
I am a concept
with a definition
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

5. GO Has Three Main Branches
cellular component
cell, cytoplasm, nucleus, …
GO: : cytosol
molecular function
binding, catalysis, …
GO: : transcription factor activity
biological process
growth, death, signaling, ...
GO: : positive regulation of metabolic process
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

6. The GO Entry for: Cell Accession:GO:0005623
Ontology:Cellular Component
Synonyms:None
Definition:The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. Source: GOC:go_curators
Comment:None
Subset:
Generic GO slim
GOA and proteome slim
Plant GO slim
Prokaryotic GO subset
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

7. GO and SGD www.yeastgenome.org
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

8. The Open Biological and Biomedical Ontologies - OBO
combine the efforts
develop orthogonal ontologies
~100 Ontologies
Ontology Lookup Service
NCBO BioPortal
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

9. GO Term Enrichment
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

10. Visualization
CSML
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

11. Ontologies Can be Used in the Semantic Web
“Find me the cellular processes that are either integral to or a refinement of signal transduction.”
Combine this with information from: Medical Ontologies, Experimental Data(bases), Wikipedia, Last.fm, … all other Triplet Store Databases
PREFIX go: <
PREFIX rdfs: <
PREFIX obo: <
SELECT DISTINCT ?label ?process
WHERE {
{ ?process obo:part_of go:GO_ } # integral to
UNION
{ ?process rdfs:subClassOf go:GO_ } # refinement of
?process rdfs:label ?label }
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

12.
Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics