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GENE ONTOLOGIESMuhammad UzairComputer Science DepartmentUniversity of TartuSupervisor: Anna Ufliand
WHAT IS AN ONTOLOGY?
There can be different forms but in general it includes:• Vocabulary of terms• Specification of meaning• Collection of labels• Relationships
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PROBLEM?
•Vast amount of biological data
•Large biology-oriented databases
•Information from different sources
“The information should make sense to biologists”
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GENE ONTOLOGIES (GO PROJECT)
Gene ontology or GO Project was established to provide a common
language to describe the biology of gene products.
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GENE ONTOLOGIES (CONT.…)
•Started in 1998 with the following three databases:• SGD (Saccharomyces Genome Database)• FlyBase• MGI (Mouse Genome Informatics )
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GOALS
1. Develop a set of controlled and structured vocabularies
2. To apply GO terms in genes or genes products in biological databases
3. To provide a centralized public resource allowing universal access
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THREE STRUCTURED TYPES:
1. Molecular Function (MF)• Catalytic or binding activities at the molecular level• Represent activities rather than entities
2. Biological Process (BP)• Describes biological goals accomplished by one or more molecular functions
3. Cellular Component (CC)• Describes locations at the levels of subcellular structures • Example: ‘nuclear inner membrane’ with they synonym ‘inner envelop’
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THE GO DATABASE
•MySQL Database – captures go content
•Perl object model and API
•Released monthly in different versions• termdb – ontologies, definitions• assocdb – association to gene products• seqdb – protein sequences
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DATABASE SCHEMA
•Models Generic graphs
•Two tables• All terms – called nodes• Term relationships – arcs
•Relationship types:• ‘is – a’• ‘part – of’
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GO DATA
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SOME STATS
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SOURCES:
GO Project - http://www.geneontology.org/
Documentation - http://www.geneontology.org/doc/GO.contents.doc.html
Software/Tools: AmiGO Browser: http://www.godatabase.org/cgi-bin/go.cgi DAG-Edit: http://www.geneontology.org/doc/dagedit_userguide/dagedit.html
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SOURCES (CONT.…)
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REFERENCES:
1. http://www.geneontology.org/
2. https://academic.oup.com/nar/article/32/suppl_1/D258/2505186/The-Gene-Ontology-GO-database-and-informatics
3. https://academic.oup.com/bib/article/1/4/398/2530008/Ontology-based-knowledge-representation-for
4. http://www.yeastgenome.org/help/function-help/gene-ontology-go
5. http://geneontology.org/slide/slide-slide
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HOMEWORK
1. Why gene ontologies are important?
2. Try to search for any gene ID in the GO project website and provide a screenshot with the searched information.
Send homework at:
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