BiologicalOntologies

BiologicalOntologies - Annotating genomes using ontologies...

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Annotating genomes using ontologies BioE131/231
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find all lactose metabolism genes find all transmembrane receptors genes what are the genes that are involved in cell migration? find all genes expressed during wing development
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text search unreliable no integration with genomic data what about new genomes? Solution: annotate using ontologies and controlled vocabularies
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Outline What is an ontology? The Gene Ontology (GO) function, process and location the GO Graph The GO Annotation model Using GO to annotate your genome
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What is an ontology? A formal representation of some domain of knowledge (e.g. anatomy, disease, biochemistry) What are the different kinds of entity which exist? How are these entities related ?
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GPCR activity G-protein coupled receptor activity transmembrane receptor activity receptor activity is_a is_a A receptor that binds an extracellular ligand and transmits the signal to a heterotrimeric G-protein complex. These receptors are characteristically seven-transmembrane receptors and are made up of hetero- or homodimers Combining with an extracellular or intracellular messenger to initiate a change in cell activity, and spanning to the membrane of either the cell or an organelle Combining with an extracellular or intracellular messenger to initiate a change in cell activity
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How are ontologies used in bioinformatics? Biological data (genes, gene products) can be annotated using terms/classes from ontologies Knowledge can be automatically transferred from experiment-rich model organisms to newly sequenced organisms, or to Homo sapiens
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OBO - Open Bio Ontologies Gene Ontology molecular function biological process cellular component Cell Ontology ChEBI - Chemical Ontology Anatomical Ontologies human, mouse, fly, worm, zebrafish Others Pathogen life cycle Pathway ontologies Sequence Ontology Phenotype and disease ontologies Organismal taxonomies http://obo.sourceforge.net
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The Gene Ontology Since 1999 Originally fly, mouse, yeast Currently 16,000 classes (terms) 6 million+ annotations covering a wide range of eukaryotes and prokaryotes D melanogaster - 11,000 out of 14,000 genes have GO annotations
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Molecular Function = elemental activity/task the tasks performed by individual gene products; examples are carbohydrate binding and ATPase activity Biological Process = biological goal or objective broad biological goals, such as mitosis or purine metabolism
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BiologicalOntologies - Annotating genomes using ontologies...

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