GO Annotation Database (GOA) – EMBL-EBI
Progress Report, Bar Harbor meeting, Sept. 2003
Summary of GO annotation/publications in 2003:
Jan 2003 Sept 2003 Difference
No. of distinct proteins 549000 730539 181539
with GO annotation
No. of GO annotations 2.7 million 3.3 million 0.6 million
No. of species with GO 49,955 58,579 8,624
No. of GO terms used Not calculated. 6584
No. of new GO term Not calculated. 105 -
% GO Coverage of 67% 79% 12%
Swiss-Prot and TrEMBL
No. of Releases GOA- Version 8.0 Version 13.0 5
No. of Releases GOA- Version 6.0 Version 11.0 5
No of Publications 4 6 2
No. of 0 2 2
Other news highlights
GOA-SPTR is increasing with help from source databases and our GO
Consortium friends. 12% increase since Jan 2003.
GOA-Human is still approx. same size (~20,000 proteins) but has
improved in quality as we re-annotate some Proteome Inc. annotations.
Changes in Ensembl protein prediction algorithm caused slump GOA-
Human in Aug. release.
New collaborations with Genome Knowledgebase should assist GOA-
Human. Huntingdons Disease and Diabetes group still working on
producing GO annotations. HUGO, waiting for feedback.
UniProt: to be cover story of NAR db issue. Picture of UniProt db plans
below. PIR staff (part of UniProt Consortium) not yet trained in GOA,
planned for 2004.
Two new GOA curators employed, Emily Dimmer and Vivian Lee
GOA curators will also be annotating IntAct (EBI interaction database).
IntAct curators will also be annotating GOA.
GOA is involved in BioCreative text mining competition. We are GO
curating 200 to 300 J. Biol. Chem. articles to generate the task 2 test
set. This data will not be released until after the evaluation (late
November). 77 JBC articles (200 proteins) already curated.
GOA-EBI and FlyBase have agreed to collaborate with ReelTwo Inc. to
validate their GO to Pubmed links in their knowledge discovery system.
Due to Biocreative Competition this validation has not started yet.
HAMAP2go mapping is finished and will be released soon. This will
help the GO annotation of microbial proteins.
2 new GOA publications in Jan 2004, NAR db issue and In silico
Integr8 Workshop included talk on GO and GOA and tutorial using
QuickGO browser, which has been updated.
AGENDA ITEM?:As a lot of GOA users are interested in GO-slim we plan to
produce Mapping of our GO annotation to generic and GOA specific slim terms
and release with GOA releases. This may also be released in SRS so that users
can retrieve all GO annotation to their query term instead of exact matches. Should
all GO Consort. release GO slim mappings in standard format??
General design of the
Automated UniProt Knowledgebase: Literature Based
Annotation Swiss-Prot + TrEMBL Annotation
UniProt Sequence Archive (UniParc)
Swiss- DDBJ/ Other
TrEMBL PIR RefSeq Ensembl PDB Patent
Prot EMBL/ Data…