PAGE 3 OF 11 Nucleic Acids Research, 2008, Vol. 36, No. 4 e22 Phospho.ELM 5.0: 2,195 sites Step 1 PhosphoSite July 2006 3,159 sites Merge “Include-all”: 5,626 sites Swiss-Prot 51.1 1,145 sites Step 2 (a) Remove sites originated from Phospho.ELM with annotation date < 12/31/04 (b) Remove sites originated from Swiss-Prot with annotation date < 10/25/05 (c) Remove curated data used in GPS and PPSP development Remaining: 3,252 sites Step 3 Assign class labels, remove redundancies 2,489 sites CDK 294 CK2 229 PKA 360 PKC 348 Other 1,258 Step 4 Make 4 balanced datasets (with negative data) CDK Positive:294 Negative:441 CK2 Positive:229 Negative:343 PKA Positive:360 Negative:540 PKC Positive:348 Negative:552 Non-phosphorylation sites 1,400 Figure 1. Procedure of compiling the MetaPS06 dataset. of the program is described. For most element prediction programs (GPS, KinasePhos, NetPhosK, PPSP and PredPhospho), Phospho.ELM (or its predecessor PhosphoBase) was used as the major data source (Table 1). The latest version of Phospho.ELM used in the development of these programs was the release of September 2004 (used in the development of GPS and PPSP). In the Phospho.ELM dataset we obtained (the May 2006 release), all entries annotated prior to 2005 are labeled with an annotation date of 31 December 2004. We removed all phosphorylation site data that originated from, or overlapped with, any pre-2005 Phospho.ELM entries from our data. For three element prediction programs—KinasePhos, NetPhosK and PredPhospho—Swiss-Prot was listed as one of the data sources. The latest version of Swiss-Prot used was Release 45.0, 25 October 2004 (used in the development of KinasePhos). All phosphorylation site data originated from, or overlapped with, any Swiss-Prot entries bearing an initial entry date prior to 25 October 2004 were eliminated from our phosphorylation site data. Three element prediction programs—GPS, PPSP and NetPhosK—used small numbers of phosphorylation sites obtained through manual curation of the literature. The curated data used in the development of GPS and PPSP were acquired from the authors of these programs through