Gene Ontology TM (GO) Consortium

Slides:

Advertisements

Similar presentations

The Gene Ontology Project: Content for the Semantic Web.

Advertisements

1 Gene Ontology and Functional Annotation Donghui Li ASPB Plant Biology, June 29, 2008, Merida.

Annotation of Gene Function …and how thats useful to you.

Applications of GO. Goals of Gene Ontology Project.

25th June 2007 Jane Lomax Using the Gene Ontology (GO) for analysis of expression data Jane Lomax EMBL-EBI.

Www. GeneOntology.org Gene Ontology Collaboration.

GO : the Gene Ontology “because you know sometimes words have two meanings” Amelia Ireland GO Curator EBI, Cambridge, UK.

Microarray Data Analysis Day 2

European Bioinformatics Institute The Gene Ontology Annotation (GOA) Database and enhancement of GO annotations through InterPro2GO Nicky Mulder

The Gene Ontology Consortium Jennifer Clark, GO Editorial Office.

Molecular & Genomic Surgery Eric M. Wilson 1/5/10.

Gene Ontology John Pinney

Introduction of bioinformatics and Biological Database 高雄醫學大學生物醫學暨環境生物學系助理教授張學偉 2006/08/08.

1 Using Gene Ontology. 2 Assigning (or Hypothesizing About) Biological Meaning to Clusters What do you want to be able to to? –Identify over-represented.

COG and GO tutorial.

Bioinformatics master course DNA/Protein structure-function analysis and prediction Lecture 13: Protein Function Centre for Integrative Bioinformatics.

Use of Ontologies in the Life Sciences: BioPax Graciela Gonzalez, PhD (some slides adapted from presentations available at

Sequence-Structure-Function Sequence Structure Function Threading Ab initio BLAST Folding: impossible but for the smallest structures Function prediction.

Internet tools for genomic analysis: part 2

Gene Ontology Project

MN-B-C 2 Analysis of High Dimensional (-omics) Data Kay Hofmann – Protein Evolution Group Week 5: Proteomics.

AP Biology Control of Eukaryotic Genes.

Using The Gene Ontology: Gene Product Annotation.

Gene Ontology (GO) Project

GO : the Gene Ontology “because you know sometimes words have two meanings” Amelia Ireland GO Curator EBI, Cambridge, UK.

GO and OBO: an introduction. Jane Lomax EMBL-EBI What is the Gene Ontology? What is OBO? OBO-Edit demo & practical What is the Gene Ontology? What is.

The aims of the Gene Ontology project are threefold: - to compile vocabularies to describe components, functions and processes - to produce tools to query.

March 24, Integrating genomic knowledge sources through an anatomy ontology Gennari JH, Silberfein A, and Wiley JC Pac Symp Biocomputing 2005:

GENE ONTOLOGY FOR THE NEWBIES Suparna Mundodi, PhD The Arabidopsis Information Resources, Stanford, CA.

Gene Ontology Consortium

1 Bio-Trac 40 (Protein Bioinformatics) October 8, 2009 Zhang-Zhi Hu, M.D. Associate Professor Department of Oncology Department of Biochemistry and Molecular.

The Gene Ontology: a real-life ontology, progress and future. Jane Lomax EMBL-EBI.

The Gene Ontology project Jane Lomax. Ontology (for our purposes) “an explicit specification of some topic” – Stanford Knowledge Systems Lab Includes:

Gene Ontology Project

Gene Ontology TM (GO) Consortium Jennifer I Clark EMBL Outstation - European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 1SD, UK Objectives:

Lecture Four: GO: The Gene Ontology ----Infrastructure for Systems Biology.

Ontologies GO Workshop 3-6 August Ontologies  What are ontologies?  Why use ontologies?  Open Biological Ontologies (OBO), National Center for.

Gene Onotology Part 1: what is the GO? Harold J Drabkin Senior Scientific Curator The Jackson Laboratory Mouse Genome Informatics.

From Functional Genomics to Physiological Model: Using the Gene Ontology Fiona McCarthy, Shane Burgess, Susan Bridges The AgBase Databases, Institute of.

24th Feb 2006 Jane Lomax GO Further. 24th Feb 2006 Jane Lomax GO annotations Where do the links between genes and GO terms come from?

Part II GO-Vocabulary of Genome. S. cerevisiae D. melanogaster.

The Gene Ontology and its insertion into UMLS Jane Lomax.

Getting Started: a user’s guide to the GO GO Workshop 3-6 August 2010.

1 Gene function annotation. 2 Outline  Functional annotation  Controlled vocabularies  Functional annotation at TAIR  Resources and tools at TAIR.

Other biological databases and ontologies. Biological systems Taxonomic data Literature Protein folding and 3D structure Small molecules Pathways and.

To Boldly GO… Amelia Ireland GO Curator EBI, Hinxton, UK.

Gene Ontology Project

Gene Ontology Consortium

Scope of the Gene Ontology Vocabularies. Compile structured vocabularies describing aspects of molecular biology Describe gene products using vocabulary.

Organization Challenges for Building Biomedical Ontologies Talk by Jennifer Clark, Slides by Michael Ashburner and Suzanna Lewis

Gene Ontology Project

Computer Science Ph. D. Seminar Gene Ontology (GO) Based Search for Protein Structure Similarity Clustering Metrics Ph.D. Candidate Steve Johnson Committee.

GO-Slim term Cluster frequency cytoplasm 1944 out of 2727 genes, 71.3% 70 out of 97 genes, 72.2% out of 72 genes, 86.1% out.

MAPPING OF SEQUENCES TO GENE ONTOLOGY. GO consortium.

Tools in Bioinformatics Ontologies and pathways. Why are ontologies needed? A free text is the best way to describe what a protein does to a human reader.

Joined up ontologies: incorporating the Gene Ontology into the UMLS.

Module 1: Gene Lists 1 Canadian Bioinformatics Workshops

Gene Annotation & Gene Ontology May 24, Gene lists from RNAseq analysis What do you do with a list of 100s of genes that contain only the following.

Canadian Bioinformatics Workshops

Sequence-Structure-Function Sequence Structure Function Threading Ab initio BLAST Folding: impossible but for the smallest structures Function prediction.

Universal descriptions of gene and gene product attributes

Annotating with GO: an overview

GO : the Gene Ontology & Functional enrichment analysis

MAPPING OF SEQUENCES TO GENE ONTOLOGY

Department of Genetics • Stanford University School of Medicine

Using the Gene Ontology (GO) for analysis of expression data Jane Lomax EMBL-EBI 25th June 2007 Jane Lomax.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

What is an Ontology An ontology is a set of terms, relationships and definitions that capture the knowledge of a certain domain. (common ontology ≠ common.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Protein Synthesis Lecture 5

Presentation transcript:

Gene Ontology TM (GO) Consortium

The problem: Vast amounts of biological data held in genome and protein databases. Different names for the same concepts in different species. Makes cross-species comparison difficult.

Ontology (for our purposes) “an explicit specification of some topic” – Stanford Knowledge Systems Lab Includes: –a vocabulary of terms (names) –defined logical relationships to each

What GO is not: Not a way of unifying databases! Not a dictated standard Additional ontologies needed to model biology and experimentation.

Molecular Function: elemental activity or task Biological Process: broad objective or goal Cellular Component: location or complex The Three Ontologies

Molecular Function: elemental activity or task DNA binding, catalysis of a reaction Biological Process: broad objective or goal Cellular Component: location or complex The Three Ontologies

Molecular Function: elemental activity or task DNA binding, catalysis of a reaction Biological Process: broad objective or goal mitosis, signal transduction, metabolism Cellular Component: location or complex The Three Ontologies

Molecular Function: elemental activity or task DNA binding, catalysis of a reaction Biological Process: broad objective or goal mitosis, signal transduction, metabolism Cellular Component: location or complex nucleus, ribosome The Three Ontologies

Go network diagram

What’s in a GO term? term : transcription initiation id : GO: definition : Processes involved in starting transcription, which is the synthesis of RNA by RNA polymerases using a DNA template.

GO: ; abscission GO: ; aging GO: ; cell differentiation GO: ; cellularization GO: ; embryonic development GO: ; genetic transfer GO: ; growth GO: ; insemination GO: ; larval development GO: ; meristem maintenance GO: ; meristem organization More examples:

GO annotation diagram

Mitochondrial P450 ( CC24 PR01238; MITP450CC24) Annotation

GO cellular component term: mitochondrial inner membrane ; GO: Where is it? Mitochondrial p450

GO molecular function term: monooxygenase activity ; GO: What does it do? substrate + O 2 = CO 2 +H 2 0 product

GO biological process term: electron transport ; GO: Which process is this?

monooxygenase activity ; GO: Other gene products: MGImonooxygenase, DBH-like 1 MGIprostaglandin I2 (prostacyclin) synthase MGIsplicing factor 3b, subunit 2 SGD flavin-containing monooxygenase TAIR FERULATE-5-HYDROXYLASE 1

mappings EC: > GO:alcohol dehydrogenase activity ; GO: EC: > GO:L-xylulose reductase activity ; GO: EC: > GO:4-oxoproline reductase activity ; GO: EC: > GO:retinol dehydrogenase activity ; GO:

Contributors FlyBase Rat Genome Database DictyBase WormBase GeneDB S. pombeCompugen Mouse Genome Database GeneDB for protozoa Genome Knowledge Base EBI GOA project TIGR Gramene The Arabidopsis Information Resource The Zebrafish Information Network Berkeley Drosophila Genome Project Saccharomyces Genome Database The Institute for Genomic Research