go : the gene ontology “because you know sometimes words have two meanings”
DESCRIPTION
GO : the Gene Ontology “because you know sometimes words have two meanings”. Amelia Ireland GO Curator EBI, Cambridge, UK. What’s in a name?. What is a cell?. Cell. Cell. Cell. Cell. Cell. Cell. Image from http://microscopy.fsu.edu. Cell. A cell can be a part or a whole organism. - PowerPoint PPT PresentationTRANSCRIPT
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GO : the Gene Ontology
“because you know sometimeswords have two meanings”
Amelia IrelandGO Curator
EBI, Cambridge, UK
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What’s in a name?
• What is a cell?
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Cell
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Cell
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Cell
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Cell
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Cell
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Cell
Image from http://microscopy.fsu.edu
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Cell
• A cell can be a part or a whole organism
Images from http://microscopy.fsu.edu
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What’s in a name?
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What’s in a name?
• Glucose synthesis• Glucose biosynthesis• Glucose formation• Glucose anabolism• Gluconeogenesis
• All refer to the process of making glucose from simpler components
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What’s in a name?
• Same name for different concepts• Different names for the same concept• Vast amounts of biological data from
different sources
Cross-species or cross-database comparison is difficult
The problem:
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What is the Gene Ontology?
• A (part of the) solution: The Gene Ontology: “a controlled
vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing”
• A controlled vocabulary to describe gene products - proteins and RNA - in any organism.
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What is GO?
• One of the Open Biological Ontologies
• Standard, species-neutral way of representing biology
• Three structured networks of defined terms to describe gene product attributes
• More like a phrase book than a biology text book
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How does GO work?
• What does the gene product do?• Where and when does it act?• Why does it perform these activities?
What information might we want to capture about a gene product?
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No GO Areas
• GO covers ‘normal’ functions and processes No pathological processes No experimental conditions
• NO evolutionary relationships• NO gene products• NOT a system of nomenclature
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Cellular Component
• where a gene product acts
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Cellular Component
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Cellular Component
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Cellular Component
• Enzyme complexes in the component ontology refer to places, not activities.
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Molecular Function
• activities or “jobs” of a gene product
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
glucose-6-phosphate isomerase activity
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Molecular Function
insulin bindinginsulin receptor activity
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Molecular Function
drug transporter activity
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Molecular Function
• A gene product may have several functions; a function term refers to a single reaction or activity, not a gene product.
• Sets of functions make up a biological process.
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Biological Process
a commonly recognized series of events
cell division
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Biological Process
transcription
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Biological Process
regulation of gluconeogenesis
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Biological Process
limb development
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Anatomy of a GO term
id: GO:0006094name: gluconeogenesisnamespace: processdef: The formation of glucose fromnoncarbohydrate precursors, such aspyruvate, amino acids and glycerol.[http://cancerweb.ncl.ac.uk/omd/index.html]exact_synonym: glucose biosynthesisxref_analog: MetaCyc:GLUCONEO-PWYis_a: GO:0006006is_a: GO:0006092
unique GO IDterm name
definition
synonymdatabase ref
parentage
ontology
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Anatomy of a GO term
• Species-specific terms use the phrase “sensu xxx” - ‘in the sense of’
• stalk formation sensu Plantae: slender or elongated
structure that supports a plant, plant part or plant organ
sensu Dictyostelium: a tubular structure that consists of cellulose-covered cells stacked on top of each other and surrounded by an acellular stalk tube composed of cellulose and glycoprotein.
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Anatomy of a GO term
• GO synonyms include alternative wordings, spellings, and related concepts Broader, narrower, exact or related Useful search aid
name: glucose transportexact_synonym: gluco-hexose transportnarrow_synonym: glucose shuttling
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Ontology Structure
• Ontologies are structured as a hierarchical directed acyclic graph
• Terms can have more than one parent and zero, one or more children
• Terms are linked by two relationships is-a part-of
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Ontology Structure
cell
membrane chloroplast
mitochondrial chloroplastmembrane membrane
is-apart-of
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GO for it!
• GO to
http://www.ebi.ac.uk/~aji/intro.html
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GO Annotation
• Using GO terms to represent the activities and localizations of a gene product
• Annotations contributed by members of the GO Consortium model organism databases cross-species databases, eg. UniProt
• Annotations freely available from GO website
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GO Annotation
• Database object gene or gene product
• GO term ID e.g. GO:0003677
• Reference for annotation e.g. PubMed paper, BLAST results
• Evidence code from evidence code ontology
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GO Annotation
• Electronic annotation from mappings files
e.g. UniProt keyword2go
High quantity but low quality Annotations to low level terms Not checked by curators
• Manual annotation From literature curation Time consuming but high quality
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GO Annotation
ISS Inferred from Sequence/Structural SimilarityIDA Inferred from Direct AssayIPI Inferred from Physical InteractionTAS Traceable Author StatementNAS Non-traceable Author StatementIMP Inferred from Mutant PhenotypeIGI Inferred from Genetic InteractionIEP Inferred from Expression PatternIC Inferred by CuratorND No Data available
IEA Inferred from electronic annotation
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GO Annotate
In this study, we report the isolation and molecular characterization of the B. napus PERK1 cDNA, that is predicted to encode a novel receptor-like kinase. We have shown that like other plant RLKs, the kinase domain of PERK1 has serine/threonine kinase activity. In addition, the location of a PERK1-GTP fusion protein to the plasma membrane supports the prediction that PERK1 is an integral membrane protein…these kinases have been implicated in early stages of wound response…
Function: protein serine/threonine kinase activity ; GO:0004674 (IDA)
Component:integral to plasma membrane ; GO:0005887 (IDA)
Process: response to wounding ; GO:0009611 (NAS)
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GO for it (again)!
• GO to
http://www.ebi.ac.uk/~aji/annotI.html