about these different gene association ﬁles and the checks that have been employed for each ﬁle. We envision that, just as for the species with much more advanced GO annotation, the GO annotations in the community gene association ﬁle will be superseded as more manually curated GO annotations become available for agricultural species. ANALYZING FUNCTIONAL DATASETS The tools currently available at the AgBase database can be divided into two categories: tools designed to assist with ana- lysis of proteomics data and tools to evaluate experimental datasets using the GO. Two tools are available at AgBase to assist with analyzing proteomics data: the proteogenomic pipeline and the ProtIDer tool. The GOProﬁler tool is designed to give a statistical summary of existing GO annota- tions. The GO suite of tools developed for functional analysis of large datasets includes GOProﬁler, GORetriever, GOanna and GOSlimViewer. This suite of tools is designed so that users can work online to analyze their large-scale datasets using GO. The proteogenomic pipeline is used to provide experimen- tally based structural annotations at a complete genome level, and the data we have obtained from proteogenomic mapping are available from the proteogenomics link at AgBase. The ProtIDer tool can be used to create a database of highly homologous proteins from ESTs and EST assemblies and is designed to assist with proteomic analysis in species which do not have genomic sequence available. In addition to providing the ProtIDer tool upon request, we will also provide organism-speciﬁc databases for proteomic analysis upon request. GOProﬁler provides an overview of current GO anno- tations available for particular species. The user provides a species taxonomy ID number (a link to a taxonomy browser is provided to assist users) and GOProﬁler returns the number of GO associations and the number of annotated proteins for that species. A separate list of unannotated proteins is also provided. GORetriever, GOanna and GOSlimViewer are designed to be used as a pipeline for analyzing functional datasets using the GO (Figure 1). GORetriever inputs a list of data- base identiﬁers and searches a set of annotated databases for existing GO annotations of protein sequences. Annotation information from designated remote databases is stored in a local database to allow fast processing of large protein datasets. GORetriever returns the data online, as a down- loadable Excel ﬁle and as a simpliﬁed text ﬁle (the GO Summary ﬁle) which can subsequently be used in GOSlim- Viewer. A list of queries without GO annotations is also provided and the user can add annotation to this list using GOanna. The GOanna tool differs from the GORetriever tool in that it does BLAST searches against a user-deﬁned local database. The GOanna tool accepts a range of inputs, including fasta ﬁles. GOanna returns up to six proteins that exceed an operator-deﬁned E-value threshold in an Excel format containing HTML links to each BLAST alignment. Users manually inspect the output and, in cases where they are satisﬁed that the query is orthologous to an annotated protein, transfer the GO annotation from the annotated Nucleic Acids Research, 2007, Vol. 35, Database issue D601 Figure 1. Analysis of functional datasets using the AgBase GO tools. Together the AgBase GO suite of tools form a pipeline for using GO to analyze microarray and other functional genomics datasets. Square boxes represent the tools, octagonal boxes are points in the pipeline that require human interpretation and ovals represent data files. GORetriever searches a set of annotated databases for existing GO annotations; sequences without annotations from GORetriever are entered into GOanna which BLAST searches a local GO database. GOanna returns up to six proteins that exceed an operator-defined E-value threshold. The user determines if the GO annotations from any of these matches can be used. Users may then choose to add literature-based or expert knowledge GO annotations to produce the final GO Summary file. GOSlimViewer can then be used to generate a high level view of the GO annotation for the proteins in a dataset using GO Slim sets. protein to their query. These data can be added to their GO Summary ﬁle. If there are no orthologous proteins with GO annotation available the user may add GO annotation by curating published literature or from expert knowledge. The ﬁnal GO Summary ﬁle is used as an input ﬁle for the GOSlimViewer tool. This tool is used to provide a high- level summary of the GO terms for a dataset and the output is a simple text ﬁle which can be charted in Excel to obtain publication quality ﬁgures. Where these tools have modest computational require- ments they are designed for online use, but all tools are freely available upon request. Each tool has comprehensive online help, including worked examples, and users are encouraged to contact us directly should they require additional information.