D110 Nucleic Acids Research, 2008, Vol. 36, Database issue Table 1. Current content of ORegAnno database Species Bos taurus Caenorhabditis briggsae Caenorhabditis elegans Ciona intestinalis Ciona savignyi Cricetinae Danio rerio Drosophila melanogaster Gallus gallus Halocynthia roretzi Homo sapiens HIV 1 Mus musculus Oryctolagus cuniculus Rattus norvegicus Saccharomyces cerevisiae Takifugu rubripes Xenopus laevis Xenopus tropicalis Totals (19 species) 6 1 7 171 171 1 13 7 1 55 15 1 1 2 680 8 6 14 948 15 738 21 194 17 1 3 2 1415 29 7834 2 215 1 99 4392 2 1 1 14 229 Regulatory haplotype Regulatory polymorphism Regulatory region Transcription factor binding site vertebrates (21). The collection of known binding sites in ORegAnno has proved an invaluable resource for the parameter optimization and estimates of accuracy for this resource. In another study, the set of known regulatory SNPs (rSNPs) in ORegAnno was used to investigate and prioritize various properties that may be important for identifying novel regulatory polymorphisms (22). The discriminatory potential of 23 properties related to gene regulation and population genetics was assessed by comparing these known rSNPs to a set of SNPs of unknown function (ufSNPs). A support vector machine classiﬁer using these properties was able to discriminate rSNPs from ufSNPs with a sensitivity and speciﬁcity of 82% and 71%, respectively (22). Finally, ORegAnno has also served a critical role in the development of new experimental approaches such as ChIP-Seq. ChIP-Seq is similar to the well-described ChIP–chip method (23) except that DNA fragments isolated from the protein– DNA complex are identiﬁed by DNA sequencing instead of hybridization to a tiling microarray. The approach was ﬁrst demonstrated for the STAT1 TF in interferon- g-stimulated HeLa S3 cells (19). A set of 41 experimentally veriﬁed sites representing 34 genomic loci for STAT1 binding were ﬁrst collected from the literature and entered into ORegAnno (Oreganno dataset: OREGDS00006). Stimulated ChIP-Seq peaks were found to overlap 24 of 34 of these loci, suggesting a sensitivity of 71%. For the ORegAnno STAT1 sites shown to be functional in HeLa cells speciﬁcally, sensitivity was 100%. The collection of known STAT1 sites and binding matrices derived from them also allowed a set of high-conﬁdence novel STAT1- binding sites to be determined and entered into ORegAnno as their own dataset (OREGDS00007). This iterative process, whereby existing data drives the creation of new data, demonstrates the utility and ﬂexibility of the ORegAnno system. Publication queue An important new feature of ORegAnno called the ‘publication queue’ was created as a literature manage- ment system to allow registered users to input relevant papers from the scientiﬁc literature as targets for annota- tion. All that is required to enter a publication is a valid PubMed identiﬁer. Optionally, a TF can be speciﬁed, allowing users to later search the queue for papers related to TFs of interest. Normally, publications are added to the queue with an entry type of ‘expert entry’, indicating that a human expert reviewed the paper and found it to be relevant. However, it is also possible to enter ‘text-mining entry’ papers (see below). A publication enters the queue with an initial state of ‘pending’. Any user can then ‘open’ the publication and begin the annotation process. Once annotated, the paper is either ‘closed’ or reset to ‘pending’ if annotation work remains. Free-form comment ﬁelds are optional for each change of state. However, when a publication is closed, one of several standardized closure comments must be chosen (success – addition of new records, failure – did not describe regulatory element, etc.). These allow the overall success rate and failure causes to be tracked. The queue can be queried on a number of ﬁelds including user, PubMed id, title, abstract, author, publication date and journal. Search results can be optionally ﬁltered by state (pending, open or closed), TF, entry type (expert or text mining) or text-mining score. Each queue record contains a history of all state changes and comments as well as links to the publication’s PubMed abstract. The current set of ‘expert entry’ papers in the queue was obtained from existing sources of curated publications including the Drosophila DNase I Footprint Database (8), REDﬂy (9), a catalog of regulatory elements for muscle-speciﬁc regulation of transcription (24,25), ABS (4), TRED (7), ooTFD (26), Totals 1 21 207 24 2 3 4 2095 37 6 22 959 2 271 1 114 4393 2 2 1 30 145