EBI is an Outstation of the European Molecular Biology Laboratory. EBI Bioinformatics Roadshow 15 March 2011 Düsseldorf, Germany Rebecca Foulger Introduction to the Gene Ontology and GO Annotation Resources
Feb 24, 2016
EBI is an Outstation of the European Molecular Biology Laboratory.
EBI Bioinformatics Roadshow15 March 2011
Düsseldorf, Germany
Rebecca Foulger
Introduction to the Gene Ontology and GO Annotation Resources
OUTLINE OF TUTORIAL:
PART I: Ontologies and the Gene Ontology (GO)
PART II: GO AnnotationsHow to access GO annotationsHow scientists use GO annotations
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
PART I: Gene Ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What’s in a name...?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Q: What is a cell?
A: It really depends who you ask!
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Different things can be described
by the same name
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• Glucose synthesis• Glucose biosynthesis• Glucose formation• Glucose anabolism• Gluconeogenesis
The same thing can be described by different names:
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Inconsistency in naming of biological concepts
• Same name for different concepts
• Different names for the same concept
Comparison is difficult – in particular across species or across databases
Just one reason why the Gene Ontology (GO) is is needed…
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Why do we need GO?
• Large datasets need to be interpreted quickly
• Inconsistency in naming of biological concepts
• Increasing amounts of biological data available
• Increasing amounts of biological data to come
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Increasing amounts of biological data available
Search on mesoderm development…. you get
9441 results!
Expansion of sequence information
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is an ontology?
• Dictionary: • A branch of metaphysics concerned with the nature and relations
of being (philosophy)
• A formal representation of the knowledge by a set of concepts within a domain and the relationships between those concepts (computer science)
• Barry Smith: • The science of what is, of the kinds and structures of objects,
properties, events, processes and relations in every area of reality.
1606 1700s
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is an ontology?
• More usefully: • An ontology is the representation of something we know about.
“Ontologies" consist of a representation of things, that are detectable or directly observable, and the relationships between those things.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is an ontology?
• An ontology is more than just a list of terms (a controlled vocabulary)• A vocabulary of terms• Definitions for those terms• *** Defined logical relationships between the terms ***
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What’s in an Ontology?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is the Gene Ontology (GO)?
A way to capture biological knowledge in a written and computable
form
Describes attributes of gene products (RNA and
protein)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The scope of GO
What information might we want to capture about a gene product?
• What does the gene product do?• Where does it act?• How does it act?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Biological Processwhat does a gene product do?
cell divisiontranscription
A commonly recognised series of events
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Cellular Componentwhere is a gene product located?
• plasma membran
e
• mitochondrion• mitochondrial membrane
• mitochondrial matrix• mitochondrial lumen • ribosome
• large ribosomal subunit • small ribosomal subunit
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Molecular Functionhow does a gene product act?
• insulin binding• insulin receptor activity
• glucose-6-phosphate isomerase activity
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Three separate ontologies or one large one?
• GO was originally three completely independent hierarchies, with no relationships between them
• As of 2009, GO have started making relationships between biological process and molecular function in the live ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Function
Function
Process
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• GO IS:• species independent• covers normal processes
• GO is NOT:• NO pathological/disease processes• NO experimental conditions• NO evolutionary relationships• NO gene products• NOT a nomenclature system
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Aims of the GO project
• Compile the ontologies
• Annotate gene products using ontology terms
• Provide a public resource of data and tools
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Anatomy of a GO termUnique identifier
Term name
DefinitionSynonyms
Cross-references
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• GO is structured as a hierarchical directed acyclic graph (DAG)
• Terms can have more than one parent and zero, one or more children
• Terms are linked by relationships, which add to the meaning of the term
node
nodenode
edge
Ontology structure
• Nodes = terms in the ontology
• Edges = relationships between the concepts
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Relationships between GO terms
• is_a
• part_of
• regulates• positively regulates• negatively regulates
• has_part
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
is_a
• If A is a B, then A is a subtype of B• mitotic cell cycle is a cell cycle• lyase activity is a catalytic activity.
• Transitive relationship: can infer up the graph
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
part_of
• Necessarily part of
• Wherever B exists, it is as part of A. But not all B is part of A.
• Transitive relationship (can infer up the graph)
BA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
regulates• One process directly affects another process or quality
• Necessarily regulates: if both A and B are present, B always regulates A, but A may not always be regulated by B
BA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• Relationships are upside down compared to is_a and part_of
• Necessarily has part
has_part
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
is_a complete
• For all terms in the ontology, you have to be able to reach the root through a complete path of is_a relationships:• we call this being is_a complete• important for reasoning over the ontology, and ontology development
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
True path rule
• Child terms inherit the meaning of all their parent terms.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How is GO maintained?• GO editors and annotators work with experts to remodel specific
areas of the ontology• Signaling• Kidney development• Transcription• Pathogenesis• Cell cycle
• Deal with requests from the community• database curators, researchers, software developers• Some simple requests can be dealt with automatically
• GO Consortium meetings for large changes
• Mailing lists, conference calls, content workshops
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Requesting changes to the ontology• Public Source Forge (SF) tracker for term related issues
https://sourceforge.net/projects/geneontology/
Why modify the GO?
• GO reflects current knowledge of biology
• Information from new organisms can make existing terms and arrangements incorrect
• Not everything perfect from the outset• Improving definitions• Adding in synonyms and extra relationships
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• Terms become obsolete when they are removed or redefined
• GO IDs are never deleted
• For each term, a comment is added to explain why the term is now obsolete
• Alternative GO terms are suggested to replace an obsoleted term
Ensuring Stability in a Dynamic Ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Searching for GO terms
http://www.ebi.ac.uk/QuickGO/
http://amigo.geneontology.org
… there are more browsers available on the GO Tools page:http://www.geneontology.org/GO.tools.browsers.shtml
The latest OBO Gene Ontology file can be downloaded from:http://www.geneontology.org/ontology/gene_ontology.obo
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Browsing the Gene Ontology using QuickGO
• Exercise 1
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
PART II: GO Annotation
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
http://www.geneontology.org
Reactome
E. Coli hub
A GO annotation is…
A statement that a gene product:
1. has a particular molecular functionOr is involved in a particular biological processOr is located within a certain cellular component
2. as determined by a particular method
3. as described in a particular reference
Accession
Name GO ID GO term name Reference Evidence Code
P00505 GOT2 GO:0004069 Aspartate transaminase activity
PMID:2731362
IDA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Evidence codes
IDA: enzyme assay
IPI: e.g. Y2H
http://www.geneontology.org/GO.evidence.shtml
review papers
subcategories of ISS
BLASTs, orthology comparison, HMMs
GO evidence code decision tree
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Gene Ontology Annotation (GOA)
The GOA database at the EBI is:
• The largest open-source contributor of annotations to GO
• Member of the GO Consortium since 2001
• Provides annotation for 321,998 species (February 2011 release)
• GOA’s priority is to annotate the human proteome
• GOA is responsible for human, chicken and bovine annotations in the
GO consortium
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GOA makes annotations using two methods
• Electronic • Quick way of producing large numbers of annotations• Annotations are less detailed
• Manual • Time-consuming process producing lower numbers of
annotations• Annotations are very detailed and accurate
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Electronic annotation by GOA
• 1. Mapping of external concepts to GO terms• InterPro2GO (protein domains)
• SPKW2GO (UniProt/Swiss-Prot keywords)
• HAMAP2GO (Microbial protein annotation)
• EC2GO (Enzyme Commission numbers)
• SPSL2GO (Swiss-Prot subcellular locations)
• 2. Automatic transfer of annotations to orthologs
Macaque Chimpanzee Guinea Pig Rat Mouse
Cow Dog Chicken
Ensembl compara
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Mappings of concepts from UniProtKB files
Aspartate transaminase activity ; GO:0004069
lipid transport; GO:006869
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Automatic transfer of annotations to orthologs
Mouse Rat Zebrafish Xenopus
Macaque Chimpanzee
Guinea Pig Rat Mouse
Dog Chicken
Human
Rat
Human
Mouse
Human
Xenopus
Tetraodon
Fugu
Zebrafish
Cow
Ensembl COMPARA
• Homologies between different species calculated
• GO terms projected from MANUAL annotation only (IDA, IEP, IGI, IMP, IPI)
• One-to-one orthologies used.
Currently provides 479,961 GO annotations for
60,515 proteins from 49 species (February 2011 release)
Manual annotation by GOA
• High-quality, specific annotations using:
• Peer-reviewed papers
• A range of evidence codes to categorize the types of evidence
found in a paper
www.ebi.ac.uk/GOA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Finding annotations in a paper
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…
Process: response to wounding GO:0009611
wound response
serine/threonine kinase activity,
Function: protein serine/threonine kinase activity GO:0004674
integral membrane protein
Component: integral to plasma membrane GO:0005887
…for B. napus PERK1 protein (Q9ARH1)
PubMed ID: 12374299
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• Qualifier
sModify the interpretation of an annotation
• NOT (protein is not associated with the GO term)• colocalizes_with (protein associates with complex but is not a bona fide member)• contributes_to (describes action of a complex of proteins)
• 'With' columnCan include further information on the method being referenced
e.g. the protein accession of an interacting protein
Additional information
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The NOT qualifier
• NOT is used to make an explicit note that the gene product is not associated with the GO term
• Also used to document conflicting claims in the literature
• NOT can be used with ALL three gene ontologies
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
In these cells, SIPP1 was mainly present in the nucleus, where it displayed a non-uniform, speckled distribution and appeared to be excluded from the nucleoli. excluded from the nucleoli
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The colocalizes_with qualifier
ONLY used with GO component ontology
Gene products that are transiently or
peripherally associated with an
organelle or complex
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Immunoblot analysis with anti-PSI polyclonal antibodies of U1 snRNP particles affinity purified from Drosophila embryonic nuclear extracts showed that PSI is physically associated with U1 snRNP (Figure 1A, top panel).
Association of U1 snRNP with GST-PSI was detected by ethidium bromide staining of the selected snRNAs and was confirmed by blot hybridization with an antisense U1 snRNA riboprobe (Figure 1C, lane 4).
PSI is physically associated with U1 snRNP
Association of U1 snRNP with GST-PSI
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The contributes_to qualifier
• Where an individual gene product that is part of a complex can be annotated to terms that describe the action (function or process) of the whole complex
• contributes_to is not needed to annotate a catalytic subunit. Furthermore, contributes_to may be used for any non-catalytic subunit, whether the subunit is essential for the activity of the complex or not
• Annotations to contributes_to often use the IC evidence code, but others may also be used.
ONLY used with GO function ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
..we next examined whether a complex of four proteins can be formed…. As shown in Figure 4, FLAG-tagged PIG-C was precipitated efficiently with anti- FLAG beads in four combinations with other proteins (Figure 4A, lanes 1–4)….. These results strongly suggest that all four proteins form a complex.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
.. To test whether the protein complex consisting of PIG-A, PIG-H, PIG-C and hGPI1 has GlcNAc transferase activity in vitro….
…incubation of the radiolabeled donor of GlcNAc, UDP-[6-3H]GlcNAc, with lysates of JY5 cells transfected with GST-tagged PIG-A resulted in synthesis of GlcNAc-PI and its subsequent deacetylation to glucosa- minyl phosphatidylinositol (GlcN-PI)
whether the protein complexhas GlcNAc transferase activity
resulted in synthesis of GlcNAc-PI andIts subsequent deacetylation to glucosa-minyl phosphatidylinositol (GlcN-PI)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Unknown v.s. Unannotated• When there is no existing data to support an
annotation, gene is annotated to the ROOT (top level) term
• NOT the same as having no annotation at all • No annotation means that no one has looked yet
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
WITH column
• The with column provides supporting evidence for ISS, IPI, IGI and IC evidence codes
ISS: the accession of the aligned protein/orthologIPI: the accession of the interacting proteinIGI: the accession of the interacting geneIC: The GO:ID for the inferred_from term WITH
column
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How to access GO annotation data
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Where can you find annotations?
UniProtKB
Ensembl
Entrez gene
Gene Association Files• 17 column files containing all information for each annotation
GO Consortium website
GOA website
GO browsers
QuickGO browser
Search GO terms or proteins
Find sets of GO annotations
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Searching for GO annotations in QuickGO
• Exercise 2• Exercise 3
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Using QuickGO to create a tailored set of annotations
• Exercise 4: Filtering• Exercise 5: Statistics
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How scientists use the GO, and the tools they use for analysis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Using GO annotations
• If you wanted to find out the role of a gene product manually, you’d have to read an awful lot of papers
• But by using GO annotations, this work has already been done for you!
GO:0006915 : apoptosis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How scientists use the GO
• Access gene product functional information
• Analyse high-throughput genomic or proteomic datasets
• Validation of experimental techniques
• Get a broad overview of a proteome
• Obtain functional information for novel gene products
•
Some examples…
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Selec ted Gene Tree: pears on lw n3d ...Branc h c olor c las s ific ation: Set_ LW_ n3d_ 5p_ ...
Co lored by : Copy of Copy o f C5_ RMA (Defa...Gene L is t: all genes (14010)attacked
time
control
Puparial adhesionMolting cycleHemocyanin
Defense responseImmune response
Response to stimulusToll regulated genes
JAK-STAT regulated genes
Immune responseToll regulated genes
Amino acid catabolismLipid metobolism
Peptidase activityProtein catabolismImmune response
Selec ted Gene Tree: pears on lw n3d ...Branc h c o lor c la s s ification : Set_ LW_ n3d_ 5p_ ...
Colored by: Copy of Copy o f C5_ RMA (Defa...Gene L is t: a ll genes (14010)
Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.
MicroArray data analysis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Validation of experimental techniques
(Cao et al., Journal of Proteome Research 2006)Rat liver plasma membrane isolation
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Analysis of high-throughput proteomic datasets
(Orrù et al., Molecular and Cellular Proteomics 2007)Characterisation of proteins interacting with ribosomal protein S19
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Obtain functional information for novel gene products
MPYVSQSQHIDRVRGAIEGRLPAPGNSSRLVSSWQRSYEQYRLDPGSVIGPRVLTSSELR DVQGKEEAFLRASGQCLARLHDMIRMADYCVMLTDAHGVTIDYRIDRDRRGDFKHAGLYI GSCWSEREEGTCGIASVLTDLAPITVHKTDHFRAAFTTLTCSASPIFAPTGELIGVLDAS AVQSPDNRDSQRLVFQLVRQSAALIEDGYFLNQTAQHWMIFGHASRNFVEAQPEVLIAFD ECGNIAASNRKAQECIAGLNGPRHVDEIFDTSAVHLHDVARTDTIMPLRLRATGAVLYAR IRAPLKRVSRSACAVSPSHSGQGTHDAHNDTNLDAISRFLHSRDSRIARNAEVALRIAGK HLPILILGETGVGKEVFAQALHASGARRAKPFVAVNCGAIPDSLIESELFGYAPGAFTGA RSRGARGKIAQAHGGTLFLDEIGDMPLNLQTRLLRVLAEGEVLPLGGDAPVRVDIDVICA THRDLARMVEEGTFREDLYYRLSGATLHMPPLRERADILDVVHAVFDEEAQSAGHVLTLD GRLAERLARFSWPGNIRQLRNVLRYACAVCDSTRVELRHVSPDVAALLAPDEAALRPALA LENDERARIVDALTRHHWRPNAAAEALGM
InterProScan
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Annotating novel sequences
• Can use BLAST queries to find similar sequences with GO annotation which can be transferred to the new sequence
• Two tools currently available;• AmiGO BLAST (from GO Consortium)
http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi• searches the GO Consortium database
• BLAST2GO (from Babelomics) http://www.blast2go.org/• searches the NCBI database
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
AmiGO BLAST
Exportin-T from Pongo abelii (Sumatran orangutan)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Numerous Third Party Tools
• Many tools exist that use GO to find common biological functions from a list of genes:
http://www.geneontology.org/GO.tools.microarray.shtml
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO tools: enrichment analysis
• Most of these tools work in a similar way:
• input a gene list and a subset of ‘interesting’ genes
• tool shows which GO categories have most interesting genes associated with them i.e. which categories are ‘enriched’ for interesting genes
• tool provides a statistical measure to determine whether enrichment is significant
• Try exercise 7 at home
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO slims
• Many GO analysis tools use GO slims to give a broad overview of the dataset
• GO slims are cut-down versions of the GO and contain a subset of the terms in the whole GO
• GO slims usually contain less-specialised GO terms
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming the GO using the ‘true path rule’ Many gene products are associated with a
large number of descriptive, leaf GO nodes:
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming the GO using the ‘true path rule’ …however annotations can be mapped up
to a smaller set of parent GO terms:
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO slims
• Custom slims are available for download;
http://www.geneontology.org/GO.slims.shtml
• Or you can make your own using;
• QuickGO• http://www.ebi.ac.uk/QuickGO
• AmiGO's GO slimmer• http://amigo.geneontology.org/cgi-bin/amigo/slimmer
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming with QuickGO
www.ebi.ac.uk/QuickGO
Map-up annotations with GO slims
Search GO terms or proteins
Find sets of GO annotations
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Map-up annotation using a GO slim
• Exercise 6
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Just some things to be aware of….• The GO is continually changing
• New terms created• Existing terms obsoleted• Re-structured• New annotations being created
• ALWAYS use a current version of ontology and annotations
• If publishing your analyses, please report the versions/dates you use:http://www.geneontology.org/GO.cite.shtml
• Differences in representation of GO terms may be due to biological phenomenon. But also may be due to annotation-bias or experimental assays
• Often better to remove the ‘NOT’ annotations before doing any large-scale analysis, as they can skew the results
ontology
annotation
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
EBI is an Outstation of the European Molecular Biology Laboratory.
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