Universal descriptions of gene and gene product attributes Gene Ontology (GO) - Universal descriptions of gene and gene product attributes 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

The Gene Ontology Project maintain and further develop its controlled vocabulary annotate genes and gene products provide tools to facilitate access 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

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? 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

What Is an Ontology? Controlled Vocabulary Taxonomy Ontology I am a concept with a definition 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

GO Has Three Main Branches cellular component cell, cytoplasm, nucleus, … GO:0005829: cytosol molecular function binding, catalysis, … GO:0003700: transcription factor activity biological process growth, death, signaling, ... GO:0009893: positive regulation of metabolic process 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

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 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

GO and SGD www.yeastgenome.org 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

The Open Biological and Biomedical Ontologies - OBO http://www.obofoundry.org/ combine the efforts develop orthogonal ontologies ~100 Ontologies Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/ NCBO BioPortal http://bioportal.bioontology.org/ 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

GO Term Enrichment 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

Visualization CSML 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

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: <http://purl.org/obo/owl/GO#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX obo: <http://www.obofoundry.org/ro/ro.owl#> SELECT DISTINCT ?label ?process WHERE { { ?process obo:part_of go:GO_0007165 } # integral to UNION { ?process rdfs:subClassOf go:GO_0007165 } # refinement of ?process rdfs:label ?label } 25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics

25.01.2011 Theoretical Biophysics - Humboldt-Universität zu BerlinPractical Bioinformatics for the Theorectical Biopysics