Ontologies
GO Workshop3-6 August 2010
Ontologies What are ontologies? Why use ontologies? Open Biological Ontologies (OBO), National
Center for Biomedical Ontology (NCBO) Some useful ontologies…
What Are Ontologies?"An ontology is an explicit specification of some topic. For our purposes, it is a formal and declarative representation which includes the vocabulary (or names) for referring to the terms in that subject area and the logical statements that describe what the terms are and how they are related to each other…
“Ontologies therefore provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary”
(From the Stanford Knowledge Systems Lab).
What Are Ontologies?“An ontology is a controlled vocabulary of well defined terms with specified relationships between those terms, capable of interpretation by both humans and computers.”
Bio-ontologies can be used to provide structured annotation.
Biocurators are biologists who are trained to catalogue biological data (using database structures, bio-ontologies, etc).
new sequencing technologies are increasing the rate that DNA is sequenced: Jan 2009: 20 billion bases (or letters) of high-
quality human DNA sequence – seven-times the length of a human genome – in 10 days. Computer analysis of the genome took another 10 days.
complexity of data is also increasing
How manage the data?- data sharing
- from data to knowledge
Why use ontologies?
Bio-ontologies are used to capture biological information in a way that can be read by both humans and computers annotate data in a consistent way allows data sharing across databases allows computational analysis of high-throughput
“omics” datasets Objects in an ontology (eg. genes, cell types, tissue
types, stages of development) are well defined.
The ontology shows how the objects relate to each other.
Why use ontologies?
Ontologies
digital identifier(computers)
description(humans)
relationships between terms
Ontology Relationships ontologies link terms using relationships relations between terms are also categorized and defined GO:
is a (eg. lyase activity is a catalytic activity) part of (eg. replication fork is part of chromosome) regulates negatively regulates positively regulates
PO: is a part of develops from
http://www.geneontology.org/GO.ontology.relations.shtml
Relationships: the True Path Rule Why are relationships between terms
important? TRUE PATH RULE: all attributes of
children must hold for all parents so if a protein is annotated to a term, it
must also be true for all the parent terms this enables us to move up the ontology
structure from a granular term to a broader term
Premise of many GO anaylsis tools
Bio-ontology requirements1. Ontology development
continual process as new terms are added to support more detailed data
2. Annotate data to the ontology computational annotation (breadth - quick) manual biocuration (depth - slow)
3. Tools that use the ontology data browsing and searching the ontology and its
associated data analysis of data annotated to the ontology
Resources for biocuration bio-ontologies (Open Biomedical Ontologies) computational pipelines (‘breadth’)
for computational annotations useful for gene products without published information
manual biocuration (‘depth’) requires trained biocurators community annotation efforts each species has its own body of literature
biocuration co-ordination MODs? Consortium? Community? biocuration prioritization co-ordination with existing Dbs, annotation, nomenclature
initiatives data updates
Current bio-ontology limitations ontology development annotation strategies to match increasing
amount of biological data computational pipelines & biocomputing community annotation/prioritization strategies biocurators
tools for dataset analysis (data complexity) cross-ontology data mining data visualization
http://obo.sourceforge.net/
The Open Biomedical Ontology is an initiative to develop bio-ontologies using common rules/principles and resources
aim to develop interoperable ontologies common relationships common evidence codes standardize file sharing
develop links between ontologies?
http://obo.sourceforge.net/
Gene Ontology Plant Ontology
Sequence OntologyTrait Ontology
Expression/Tissue OntologiesInfectious Disease Ontology
Cell Ontology
Genomic Annotation Genome annotation is the process of
attaching biological information to genomic sequences. It consists of two main steps:
1. identifying functional elements in the genome: “structural annotation”
2. attaching biological information to these elements: “functional annotation”
biologists often use the term “annotation” when they are referring only to structural annotation
Structural & Functional Annotation
Structural Annotation: Open reading frames (ORFs) predicted during genome
assembly predicted ORFs require experimental confirmation Sequence Ontology Project (SO): provide for a structured
controlled vocabulary for the description of primary annotations of nucleic acid sequence
Functional Annotation: Gene Ontology (GO): annotation of gene product function initially, predicted ORFs have no functional literature and GO
annotation relies on computational methods (rapid) functional literature exists for many genes/proteins prior to
genome sequencing
Functional annotation usingGene Ontology
Nomenclature(species’ genome nomenclature committees)
Other annotations
using other bio-ontologies e.g.
AnatomyOntology
Structural Annotationincluding Sequence Ontology
Genomic Annotation
Gene Ontology (GO) Not about genes!
Gene products: genes, transcripts, ncRNA, proteins
The GO describes gene product function Not a single ontology
Biological Process (BP or P) Molecular Function (MF or F) Cellular Component (CC or C)
Gene Ontology (GO) de facto method for functional annotation Widely used for functional genomics (high
throughput) Many tools available for gene expression
analysis using GO The GO Consortium homepage:
http://www.geneontology.org
Plant Ontology (PO) describes plant structures and growth and
developmental stages Currently used for Arabidopsis, maize, rice – more
being added (soybean, tomato, cotton, etc) Plant Structure: describes morphological and
anatomical structures representing organ, tissue and cell types
Growth and developmental stages: describes (i) whole plant growth stages and (ii) plant structure developmental stages
The PO Consortium homepage:
http://www.plantontology.org/
PO Browser – based on the GO Consortium browser, Amigo
http://www.ebi.ac.uk/ontology-lookup/