D654 Nucleic Acids Research, 2011, Vol. 39, Database issue collating information about proteinaceous spider toxins. Since its establishment in 2009, ArachnoServer has been widely used and the website has hosted visitors from more than 60 countries. ArachnoServer toxin cards (see Figure 1 for an example) are now cross-referenced through links on the corresponding sequence records in UniProtKB (http://www.uniprot.org), ArachnoServer accession numbers are included in the UniProtKB mapping service and the UniProtKB records have adopted the rational toxin nomenclature (1) that has been applied universally in ArachnoServer. DATA SOURCES AND CURATION The starting point for data curation in ArachnoServer is the automated collection of all publically available sequence and annotation information for spider toxins from UniProtKB (10), the International Nucleotide Sequence Database Collection (INSDC) and the Protein Data Bank (PDB) (11). These data sets are joined with the assistance of the Sequence Retrieval System (SRS) (12) into a single non-redundant set containing peptide sequences, nucleotide sequences and protein structures (where available) for each toxin (Figure 2). Other database identiﬁers (e.g. NCBI taxonomy codes, Gene Ontology classiﬁcations, PROSITE and Pfam accessions, etc.) are also imported, as well as literature references, annotations of sequence and structure features (e.g. known locations of disulﬁde bonds) and toxin descriptions. Spider taxonomy is derived from the World Spider Catalog (13) while other taxonomy (used for classiﬁcation of a toxin’s phyletic selectivity) is from the NCBI Taxonomy database (14). Since the majority of spider toxins act on ion channels and cell-surface receptors (8,15), we developed a molecular target ontology speciﬁ- cally for venom toxins that is based on the channel and receptor subtype deﬁnitions and nomenclature recommended by the International Union of Basic and Clinical Pharmacology (IUPHAR) (16). Using the curation interface within ArachnoServer, curators can add additional data which includes, but is not limited to, a detailed description of the toxin; toxin name [which conforms to the rational nomenclature proposed for venom peptides (1) and venom sphingo- myelinases (17)]; source species; discovery date; toxin synonyms; biological activity; phyletic speciﬁcity; molecular targets; sequence features such as toxin pharmacophore and disulﬁde bonds; database cross- references; and literature references. Literature references are sourced from PubMed (where available) using the PubMed eFetch web service. The process of data retrieval and curation in ArachnoServer is summarized in Figure 2. IMPLEMENTATION ArachnoServer is a Java Spring Model-View-Controller web application, built using a Hibernate Object Relational Model interfacing to a MySQL database. The web interface utilizes Asynchronous JavaScript and XML (AJAX) and dynamically generated HTML pages from server side JSP scripts to provide a rich application environment for both curation and public access. Care has been taken to ensure that the search, browse and BLAST features are powerful and intuitive. All major web browsers are supported. IMPROVED FEATURES IN ARACHNOSERVER 2.0 In response to user feedback, we have implemented a major upgrade of ArachnoServer that includes the following new features: Molecular mass Mass spectrometry is becoming one of the standard methods used to characterize venom components (7). Most spider toxins contain multiple disulﬁde bonds and therefore the mass of the oxidized form of the peptide (as opposed to the reduced form that is calculated in most databases) is typically of primary interest to venom researchers. Thus, toxin records in ArachnoServer now provide the average and monoisotopic masses for both the reduced and oxidized form of the toxin (see Figure 1 for an example). Moreover, the advanced search feature now includes an option to perform a search based on any of these mass classes (see below). Improved advanced search ArachnoServer provides an Advanced Search feature that enables multiple search clauses to be grouped and joined using Boolean operators. We have now added the ability to search for toxins on the basis of toxin mass, external database accession numbers and the date on which the toxin record was published in ArachnoServer. Additional columns have been added to the table of search results that display context-speciﬁc data for certain search categories. For example, a search for toxins with oxidized molecular masses within a certain mass range will yield a table in which the oxidized molecular mass for each ‘hit’ is indicated in the additional column. Context-speciﬁc data columns have also been introduced for searches based on toxin discovery date as well as the number of solved PDB structures, number of biological activities, number of molecular targets, number of posttranslational modiﬁcations and number of disulﬁde bonds. Search results can be exported in both PDF and XML formats. Additional BLAST capabilities Rapid BLAST searches based on the mature toxin sequence ‘only’ can now be performed directly from the toxin card. This option provides a mechanism to enrich alignment results for mature toxin sequences. The option to perform a BLAST search using the entire toxin sequence, which may include signal and propeptide regions, is still available. BLAST results are formatted in HTML and contain links to ArachnoServer toxin cards and the corresponding UniProtKB records where available.