GO News Archive
More recent news can be found in the GO newsletter. News from 2001 and earlier can be found in the GO.what_is_new file (plain text)
2006
GO Annotation Camp announcement
April 14, 2006
The GO Consortium will hold a GO Annotation Camp at the Tresidder Memorial Union (Oak Lounge), Stanford University, CA, this summer. The training portion of the Camp will be three days long from Wednesday, July 12 through Friday, July 14. More information is available in the General Information, Working Schedule, and Registration pages.
GO content meeting minutes available
January 9, 2006
The minutes from the GO Content Meeting held at TIGR on November 15-16, 2005 to discuss the development of the immunology terms in GO are now available.
2005
GO gene associations now quality control filtered
October 27, 2005
As of October 10th, the GO gene association information distributed via AmiGO and our FTP, HTTP and CVS services is being subjected to a quality control filter prior to release. The filtering removes duplicate annotations by allowing only a single database authority for each genome, as well as removing obsolete GOIDs and any information that does not match the format specification. The GO database data files for October were built using the non-redundant data. See the GO annotation guidefor more information.
GO Annotation Camp minutes available
September 21, 2005
The minutes from the GO Annotation Camp held at Stanford University from June 1-4, 2005 are now available, in either PDF or TEXT formats, from the /meeting/minutes/ directory of the GO ftp site.
EBI GO annotator position
June 30, 2005
A GO annotator position has become available with the GOA group at the European Bioinformatics Institute in Cambridge, UK. See GO job opportunities for more information.
GO Users Meeting at MGED 8
May 2, 2005
We are pleased to announce the 2005 GO Users Meeting will be held as part of the MGED 8 meeting in Bergen, Norway, in mid September. See the meeting information page for more on the meeting and to submit your abstract.
GO Annotation Camp
April 1, 2005
A GO Annotation Camp will be held at Stanford University from 9 am Wednesday, June 1st until noon on Saturday, June 4th. Please visit the meeting website for more details.
Prokaryotic GO slim available
February 8, 2005
For those users of GO who would rather not view eukaryote-specific terms (such as mitochondrial and nuclear terms), we now have available as part of the OBO format ontology file a new category of GO terms: a prokaryotic subset used to filter out eukaryotic terms.
2004
GO slims now in the OBO flat file
July 21, 2004
We are pleased and excited to announce that the four current GO slims, those for plant, yeast, GOA and the generic GO slim, have now been incorporated into the OBO-format flat file. Whilst we will continue to generate GO slims in the old format, we would encourage users to take advantage of the new OBO format for all their GO slim needs.
Reactome dbxrefs added to GO.
July 12, 2004
We are pleased to announce that a mapping of Reactome biological processes to GO terms has been added to the external2go directory.
Chicago users meeting first announcement.
June 10, 2004
We are pleased to announce the next Gene Ontology Users Meeting on Thursday, October 14, 2004 at Northwestern University's Chicago campus. The deadline for abstract submission is September 17, 2004, and the deadline for registration is October 1, 2004. Please visit the meeting website for more information.
Mapping of cog2go now available.
June 10, 2004
A mapping of COG (Clusters of Orthologous Groups) functional categories to GO terms has been added to the external2go directory.
OBO flat file format now available.
February 16, 2004
The new OBO flat file format is now available. GO files will be released in both the new OBO format and the older GO flat file format. The new format has several advantages including easier parsing, improved extensibility and smaller file sizes.
2003
September meeting minutes available.
November 27, 2003
The minutes from the September 2003 GO meeting at Bar Harbor are now available from the meetings web site and the GO ftp site.
MultiFun gene classification system mapped to GO terms
October 3, 2003
A mapping of MultiFun (a classification system for the cellular/physiological roles of E. Coli gene products) to GO terms has been added to the go/external2go directory.
Changes to molecular function terms
Feburary 5, 2003
All GO molecular function term names are to be appended with the word 'activity' on March 1 2003.
2002
ZFIN annotations available
December 9, 2002
The first set of GO annotations for the zebrafish (Danio rerio) has been provided by ZFIN. The file is available from the usual GO FTP, HTTP, and CVS resources.
- FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin
- HTTP: http://www.geneontology.org/cgi-bin/GO/downloadGOGA.pl/gene_association.zfin
Users Meeting archive page
December 3, 2002
A new web page stores links to information (e.g. programs, abstracts) about past GO Users Meetings.
Update on annotations: newly annotated species
October 24, 2002
Annotation files have been released over the past few months for several species; see the go/gene-associations/ directory for the following new files:
- Glossina morsitans (tsetse fly) gene_association.GeneDB_tsetse
- Oryza sativa (rice) gene_association.gramene_oryza
- Trypanosoma brucei gene_association.GeneDB_Tbrucei and gene_association.tigr_Tbrucei_chr2
- Vibrio cholerae gene_association.tigr_vibrio
MIPS Functional Catalogue mapped to GO terms
August 27, 2002
A mapping of MIPS Functional Catalogue entries to GO terms has been added to the go/external2go directory.
All GOA data from EBI published.
June 21, 2002
GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The project announces the release of all GO annotations that exist in SWISS-PROT and TrEMBL as well as a third release of annotation for the SWISS-PROT/TrEMBL/Ensembl non-redundant human proteome set.
This release represents a considerable contribution to the GO Consortium annotation effort providing over 2 million GO associations across 481422 SWISS-PROT and TrEMBL entries covering 43239 species.
The data can be obtained via:
EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
EBI SRS: http://srs.ebi.ac.uk. Search GOA data library where both
GOA SPTr and GOA Human association files have been merged.
GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/
For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk.
Enjoy!
New evidence code inferred by curator (IC).
June 5, 2002
GO has added a new evidence code, "inferred by curator," for those cases where an annotation is not supported by any evidence, but can be reasonably inferred by a curator from other GO annotations, for which evidence is available.
February meeting minutes available.
April 26, 2002
The minutes from the February meeting of the GO Consortium, organized by SGD and sponsored by O'Reilly and Associates at The Westin La Paloma in Tucson, AZ, are now available from the CVS repository and from the ftp site (ftp://ftp.geneontology.org/pub/go/meeting/minutes/).
SourceForge curator requests tracker system now active.
March 20, 2002
The SourceForge system for tracking curator requests is now in use. There are also some instructions for using the system.
XML and MySQL repository to be located only at Berkeley.
March 6, 2002
As agreed at the October meeting of the GO Consortium, the latest versions and archives of the monthly releases of the MySQL and XML releases will now be kept only at UC Berkeley for the best access to the most up to date files. The links on the GO home page now point only to the MySQL and XML repository at Berkeley. The copies at Stanford will be removed from the CVS repository and from the ftp site; specifically, this file will be removed: ftp://ftp.geneontology.org/pub/go-xml/go.xml
GO and RESID now reciprocally cross-linked.
January 4, 2002
As announced on September 20 2001 John Garavelli and I have been working to cross-link his RESID database of modified amino acids to GO. This has now been completed and updated to version 28.00 of the RESID database (available from ftp://ftp.ncifcrf.gov/pub/users/residues/). This release contains 311 records and these are cross-linked to GO in Xref lines. GO has created "biological_process" terms relevant to these modified residues and the cross-links from GO to RESID are stored in the definitions (GO.defs) of these terms.
October meeting minutes available.
January 3, 2002
The minutes from the October meeting of the GO Consortium, hosted by DictyBase at Northwestern University, are now available from the CVS repository and from the ftp site (ftp://ftp.geneontology.org/pub/go/meeting/minutes/).