D600 Nucleic Acids Research, 2007, Vol. 35, Database issue Transcriptome data allow annotation of RNA termini, splice junctions and untranslated RNAs. In addition, quantitative processes at the RNA level are independent of the protein level. However, detection of an mRNA is not conclusive evi- dence that the gene has a protein product (16). Proteogenomic mapping uses high-throughput mass spectrometry-based methods to provide direct evidence for the existence of proteins in vivo (15,17–19) and their locations in cells (20). Proteomics also more accurately determines the boundaries of functional ORFs and identiﬁes unknown ORFs that cannot be well established on the basis of homology. In contrast to the structural genome, which is considered to be ﬁxed (at least in the short term), the functional genome rapidly changes both quantitatively and qualitatively in response to the environment. Understanding the functional genome informs us how genes function together. Genome functional annotation describes, interprets and explains the functions of the gene products themselves. The Gene Onto- logy (GO) project (21) provides the basis for the design, development and implementation of publicly available, expertly curated databases containing comprehensive genome functional annotations using controlled structured vocabu- laries (ontologies). First-pass electronic GO annotation (‘inferred by electronic annotation’ or IEA) is performed by data mining external sources of gene product information such as InterPro domains and SwissProt keywords. Anno- tations ‘inferred from sequence or structural similarities’ (ISS; e.g. by BLAST searches) and IEA rapidly provide ‘breadth’ and are especially valuable for organisms with little intensive manual GO curation. All other annotations are performed by expert curators using species-speciﬁc litera- ture or (rarely) expert knowledge and these GO annotations are considered to be the ‘gold standard’ (22–24). To facilitate functional analysis in agriculturally important genomes we launched the AgBase database. The AgBase database is a curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agri- cultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. ACCESSING INFORMATION FROM AgBase The AgBase database provides experimentally derived structural annotations, GO annotations and tools for analy- zing functional genomics data. Structural annotations based on proteogenomic mapping are provided as expressed pep- tide sequence tags or ‘ePSTs’ (20) and the proteogenomic pipeline used to generate these ePSTs from proteomic data is freely available upon request. AgBase curators provide manually curated GO annotations. We work in collaboration with the European Bioinformatics Institute GOA project [EBI-GOA (25)] and speciﬁcally focus our efforts on providing GO annotations for gene products EBI-GOA has not automatically annotated using IEA. The AgBase gene detail page displays GO annotations from both AgBase and EBI-GOA and the group responsible for each GO anno- tation is attributed. Gene association ﬁles of gene products annotated by AgBase are available for download in a tab-delimited format. Through EBI-GOA our GO anno- tations are added to the GO and UniProtKB databases (21,26). Tools developed by the AgBase consortium are made freely available upon request and where possible are web-based. Tools are designed to analyze large datasets generated by functional genomics based approaches. The AgBase database can be accessed directly via http://www. agbase.msstate.edu, or where appropriate the NCBI Genome Resources pages provide links to GO databases at AgBase. Users can access information by text searches of protein or gene names, text searches of GO terms, searching via a variety of accession numbers or via BLAST searches. The AgBase tools also access the AgBase database. Users can choose to search the entire AgBase database or narrow their search by choosing an organism-speciﬁc database. The text search performs an exact substring search and multiple queries are also supported. Searches based on UniProtKB accessions and identiﬁers, UniParc identiﬁers, EMBL acces- sions, InterPro identiﬁers and NCBI non-redundant protein database GenBank gi numbers are supported. A BLAST based search is also available in instances where the user has sequences not represented in these databases or for which there is no database accession. To facilitate data mining the user has the option of searching the AgBase database by taxon ID or using either GO term names or identiﬁers. The proteogenomic database may also be searched using either text or BLAST based searches. A TWO TIER SYSTEM OF GO ANNOTATIONS Our AgBase download page provides a ‘GO Consortium’ gene association ﬁle containing fully quality checked annota- tions supported by the GO Consortium and a ‘Community’ gene association ﬁle containing annotations checked only for formatting errors by the AgBase biocurators following GO Consortium guidelines (http://www.geneontology.org/ GO.annotation.shtml#script). This two-tiered system allows users to choose the breadth of GO coverage most appropriate for their experimental needs. The community gene association ﬁle contains three kinds of annotations: (i) GO annotations for ‘predicted proteins’ without Uni- ProtKB identifiers that until 10 July 2006, were not supported by EBI-GOA. (ii) ISS annotations to evidence codes that stopped being accepted as of April 2006. For example, we recently completed ISS annotation of 1609 sheep proteins in UniProtKB that had no GO annotation but fewer than half will be released into the UniProtKB database following the newest GO Consortium guidelines. (iii) GO annotations from community researchers that have not yet been quality checked by a trained GO curator. This type of annotation will be transferred to the GO Consortium gene association file after quality checks by AgBase biocurators and the original submitter be acknowledged in this gene association file. Documentation is provided at the AgBase download site and via a link from the AgBase gene detail page informing users