Outline

1
Gene Ontology Annotation (GOA)
Implementation of GO in SWISS-PROT, TrEMBL and
InterPro
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Aims of GOA project

• To associate GO terms with All proteins in
• - SWISS-PROT TrEMBL
• - InterPro families and domains
• (ClusTr Groupings, CDSs in EMBL)
• Fast tracking GO annotation of completed
• proteomes eg. human

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Q10561
Large-scale GO annotation

• SWISS-PROT Keyword lt-gt GO term mapping
• EC number lt-gt GO term mapping
• InterPro entry lt-gt GO term mapping

SP_KWFatty acid biosynthesis gt GOfatty acid
biosynthesis GO0006633
EC6.4.1.2 gt GOacetyl-CoA carboxylase
GO0003989
InterProIPR000438 Acetyl-CoA carboxylase
carboxyl transferase beta subunit gt
GOacetyl-CoA carboxylase GO0003989
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Electronic GO Annotation
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Electronic Annotation Status
Evidence Source Annotations Proteins
IEAIPRO 1 244 525 413 379
IEASPKW 1 012 768 368 328
IEASPEC 164 413 72 521
IEA Total Human 2 415 659 44 254 517 152 16 180

Nov 2002
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Enter SPTR Accession No.
Enter Evidence Code

Enter Reference Type
Enter Reference Accession No
Existing mappings (IPRO,SPKW, SPEC, PINC)
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8

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Converting SWISS-PROT free text to GO terms

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Manual Annotation Status
Evidence Source Annotations Proteins
Non-IEATotal Human gt 31 000 30 458 gt 10 000 9 075
All CodesTotal Human 2 464 507 74 712 522 844 18 563

Nov 2002
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How did we perform?

• Electronic Manual
• 57 1.3
• 45668 species 151 species
• 2.46 mill assoc. 522844 proteins
• InterPro Keyword Manual

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GOA Dataflow
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Annotation File Format

• gene association file

SPTR O00505 IMA3_HUMAN GO0006886 GOAinterpro IEA
P SPTR O00505 IMA3_HUMAN GO0005634 GOAspkw IEA
C SPTR O00505 IMA3_HUMAN GO0005643 PUBMED9154134
TAS C
Importin alpha-3 subunit IPI00012092 protein taxon
9606 20020920 Importin alpha-3
subunit IPI00012092 protein taxon9606
20011011 Importin alpha-3 subunit IPI00012092 prot
ein taxon9606 20020630
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Data Searching Retrieval

• Gene Association File
• ftp//ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gen
  e_association.goa
• ftp//ftp.geneontology.org/pub.go/gene-association
  s/gene_association.goa
• QuickGO or AmiGO Browser
• SRS (GO, GOA)
• InterPro
• Proteome Analysis Pages
• GO MySQL at BDGP
• http//www.fruitfly.org/cgi-bin/wiki/view.pl/GoWeb
  /GoExampleQueries
• Ensembl GOview
• AltExtron DB
• GOA home page
• http//www.ebi.ac.uk/GOA

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Data Searching Retrieval

• QuickGO Browser

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GOBO contribution
SP Tisslist
Oxf. Dict., MGED
GO
GO
GO
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Find the location of human genes mapped to a
particular GO term using ensembl GO-View.
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SRS Functional Queries Across DB
A
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InterPro
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Proteome Analysis Pages
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Distribution of Molecular Function
Sept 2002
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What can I do with GOA?

• Structured vocabularies support semantic
  integration within the EBI system and promote
  broader integration of knowledge from the
  SWISS-PROT database group.
• Discover the function of new sequences by
  determining more quickly functional similarities
  among proteins.
• Perform functional queries across our data
  repositories
• Overview proteomes with GO-slim
• Incorporate our manual annotations into your
  database -
• to enhance your dataset or use it to validate
  an automated way of deriving information about
  protein function
• Use our mappings to map GO terms to your own
  dataset
• (microarray/mass spec.)

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Using GO for functional genomics

• Allows cluster analysis, e.g expression data,
• microarrays etc

component
process
function
Gene
experimental condition
genes
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Future of GOA

• GO is dynamic, GOA needs regular updating
• Regular release Human(v5) and SPTR(v3)
• GOA file
• Incorporate manual annotations from other grps
• Display of GOA in TrEMBL XML, other EBI db eg.
  EMBL
• GO Curation tool and QuickGO browser being
  updated
• Accessing GOA via SRS needs updating.
• By 2004 -gt 70 SWISS-PROT TrEMBL w GO ?

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Acknowledgements
Daniel Barrell GOA File updates David Binns
QuickGO Wolfgang Fleischmann Automation
Coordinator John Maslen - Talisman Paul Kersey
Xref file data set generation Michele Magrane
all curators - GO Annotation Nicola Mulder Co -
InterPro Midori Harris, Jane Lomax, Amelia
Ireland, Cath Brooksbank GO Curators Evelyn
Camon GOA Coordinator BioBabelQLRT-2000-00981
TEMBLORQLRI-2001-00015 NIH1R01HG2273-01
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Standards and Ontologies for Functional Genomics
(SOFG) 1720 Nov 2002 Towards unified
ontologies for describing biology and
biomedicine www.wellcome.ac.uk/hinxton/sof
g