2.1 Simple searching
QuickGO users can view and search information provided for GO terms (identifiers, words/phrases in the title or definition, cross-references and synonyms), as well as protein data from UniProtKB (accession numbers, names and gene symbols). Results are ranked so that terms most closely matching the query are returned first. Individual words and combinations of words are scored according to the field in which they occur and their frequency within GO.
When a GO term is selected, QuickGO presents a tabbed view of the term's information (including definition, cross-references and child terms). Interactive graph and table views of the term's position in the GO as well as a page displaying all annotations to the selected term are presented. Statistics for each GO term are available, showing which terms are frequently concurrently annotated, aiding curators to annotate consistently.
QuickGO is updated weekly with protein names, gene symbols, accessions and taxonomy data from UniProtKB. Single or multiple protein accessions can be queried and selected proteins will display all associated GO annotations, both electronic and manual.
2.2 Annotation download facility
The GOA annotation set is a central component of QuickGO that can be filtered using multiple combinations of parameters. Tailoring annotation sets has become increasingly necessary as the number of GO annotations to new sequences has increased rapidly, causing users to be overwhelmed when downloading and filtering the GOA-UniProt gene association file (2.2 GB in July 2009).
In total, nine different parameters are available for users to create their desired subset of annotations. Filtering options include:
Specific protein(s): users can submit lists of identifiers and map between identifier types (e.g. UniProtKB, Ensembl, RefSeq, MGI and FlyBase identifiers). Over 14 million identifiers are available.
Evidence codes: annotations can be selected for specified evidence codes, for example, representing results from electronic (IEA) or experimental methods (IMP, IGI, IPI, IDA, IEP and EXP).
Qualifier data: qualified annotations can be filtered, for example, negative (‘NOT’) annotations can be removed.
Taxonomic data: As QuickGO uses the UniProtKB taxonomic hierarchy, it can provide annotation sets for large taxonomic groups, e.g. all flowering plants, or for a single species.
: annotations using selected GO terms can be viewed (see also Section 2.3
for GO slim).
More complex queries are made using the advanced search allowing users to apply a combination of Boolean operators (AND, NOT, OR) to their queries.
Once an annotation set has been selected, QuickGO provides a paginated view of annotations and statistics. Statistics are calculated on-the-fly, and provide detailed summaries of, e.g. the distribution of GO terms or evidence codes present in the specified dataset (B). Much of the data in the annotation table is clickable (including GO terms, taxonomy information, identifiers) to provide further information or links to relevant web pages. Finally, users can specify the format of their downloaded data; either in gene association, FASTA (sequences) or gene2go (NCBI standard for annotations) formats or alternatively as a list of protein/gene identifiers (A).
Fig. 1. (A) Protein Annotation view. (1) Filtering options. (2) Statistics. The table contains all the information for a protein-GO term association, including: (3) names and identifiers of GO terms; (4) reference for the annotation; (5) GO evidence code for (more ...)
2.3 GO slim generation and annotation mapping
QuickGO not only filters annotations to a specific set of GO terms, but also allows the reaction or adaption of GO slims. Users can collect a set of GO terms, view them as a graph and use them to construct a GO slim. Annotations can be ‘mapped up’ or ‘slimmed’ to these selected GO terms. Predetermined GO slims created by groups in the GO Consortium are also provided. These combined facilities allow users to extensively tailor both the GO slim sets and the associated GO annotations (http://www.ebi.ac.uk/QuickGO/GMultiTerm
2.4 Web services
All data provided by QuickGO can be queried remotely, both for GO term information and annotation data. These web services are fully integrated, so that the filtering options and datasets available are fully synchronized between the browsable and web service interfaces. The web services have been designed for ease of use, providing a REST-style query interface with results displayed in standard compliant gene association, OBO or XML formats.