LinkPhinder benchmarking splits

Benchmarking splits used to evaluate the LinkPhinder and other protein phosphorylation prediction models. <br>The XY numbers in the benchmark folder names reflect the train-test data ratio (e.g. 'benchmark9010' means the training and testing data are 90% and 10%, respectively, of the benchmark dataset). The nZ number then means the number of negatives per each positive (e.g. 'benchmark7030n10' means a 70/30 train/test split with ten negatives per each positive). PhosphoSitePlus (https://doi.org/10.1093/nar/gku1267) was used as the benchmark dataset in most cases, with the exception of folders tagged with 'cutillas20' (this is based on the kinase-substrate interaction dataset published in https://doi.org/10.1038/s41587-019-0391-9). The columns in the training and testing split files correspond to the kinase, site, and substrate respectively. The columns in the scores files correspond to the kinase uniprot accession id, the site, the substrate uniprot accession id and the LinkPhinder score respectively.

本基准拆分集用于评估LinkPhinder及其他蛋白质磷酸化预测模型。基准文件夹名称中的XY数字代表训练集与测试集的数据占比（例如"benchmark9010"表示训练集与测试集分别占基准数据集的90%与10%）。后缀"nZ"中的Z则代表每个正样本对应的负样本数量（例如"benchmark7030n10"表示训练测试拆分比例为70/30，且每个正样本对应10个负样本）。多数情况下以PhosphoSitePlus（https://doi.org/10.1093/nar/gku1267）作为基准数据集，仅带有"cutillas20"标签的文件夹除外——该类文件夹基于2019年发表于https://doi.org/10.1038/s41587-019-0391-9的激酶-底物相互作用数据集构建。训练集与测试集拆分文件的列依次对应激酶、位点与底物。得分文件的列依次对应激酶的UniProt登录号、位点、底物的UniProt登录号以及LinkPhinder得分。