CoCoScore Supplementary Data v1.0

Supplementary Data: CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision # Text mining dictionaries The entities file (entities.tsv.gz), names file (names.tsv.gz), and groups file (groups.tsv.gz) were used to identify proteins/genes, diseases, and tissues in the PubMed + PMC corpus.Please check the following README for usage of these files: https://bitbucket.org/larsjuhljensen/tagger/src/default/README.md # Datasets and pre-trained sentence classification models ## H. sapiens disease-gene associations Training dataset: dataset_9606_-26_train.tsv.gzTest dataset: dataset_9606_-26_test.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_9606_-26.ftz ## H. sapiens tissue-gene associations Training dataset: dataset_9606_-25_train.tsv.gzTest dataset: dataset_9606_-25_test.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_9606_-25.ftz ## H. sapiens functional protein-protein associations Training dataset: dataset_9606_9606_train.tsv.gzTest dataset: dataset_9606_9606_test.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_9606_9606.ftz ## D. melanogaster functional protein-protein associations Training dataset: dataset_7227_7227_train.tsv.gzTest dataset: dataset_7227_7227_test.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_7227_7227.ftz ## S. cerevisiae functional protein-protein associations Training dataset: dataset_4932_4932_train.tsv.gzTest dataset: dataset_4932_4932_test.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_4932_4932.ftz ## H. sapiens physical protein-protein interactions Training dataset: dataset_9606_9606_train_physical.tsv.gzTest dataset: dataset_9606_9606_test_physical.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_9606_9606_physical.ftz ## D. melanogaster physical protein-protein interactions Training dataset: dataset_7227_7227_train_physical.tsv.gzTest dataset: dataset_7227_7227_test_physical.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_7227_7227_physical.ftz ## S. cerevisiae physical protein-protein interactions Training dataset: dataset_4932_4932_train_physical.tsv.gzTest dataset: dataset_4932_4932_test_physical.tsv.gzfastText Sentence classification models trained on training dataset: ft_model_CoCoScore_pretrained_4932_4932_physical.ftz # Pre-trained word embeddings Pre-trained fastText word embeddings can be found in: fasttext_sg_masked_dim_300_epoch_5_lr_0.05_minn_3_maxn_6_ws_5.vec.gz# 补充数据：CoCoScore：基于远程监督的文本挖掘应用上下文感知共现评分方法 ## 文本挖掘词典 实体文件（entities.tsv.gz）、名称文件（names.tsv.gz）与分组文件（groups.tsv.gz）用于识别PubMed及PMC文献库中的蛋白质/基因、疾病与组织。相关文件的使用方法请参阅以下README文档：https://bitbucket.org/larsjuhljensen/tagger/src/default/README.md ## 数据集与预训练句子分类模型 ### 智人（H. sapiens）疾病-基因关联数据集 训练集：dataset_9606_-26_train.tsv.gz 测试集：dataset_9606_-26_test.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_9606_-26.ftz ### 智人（H. sapiens）组织-基因关联数据集 训练集：dataset_9606_-25_train.tsv.gz 测试集：dataset_9606_-25_test.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_9606_-25.ftz ### 智人（H. sapiens）功能型蛋白质-蛋白质关联数据集 训练集：dataset_9606_9606_train.tsv.gz 测试集：dataset_9606_9606_test.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_9606_9606.ftz ### 黑腹果蝇（D. melanogaster）功能型蛋白质-蛋白质关联数据集 训练集：dataset_7227_7227_train.tsv.gz 测试集：dataset_7227_7227_test.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_7227_7227.ftz ### 酿酒酵母（S. cerevisiae）功能型蛋白质-蛋白质关联数据集 训练集：dataset_4932_4932_train.tsv.gz 测试集：dataset_4932_4932_test.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_4932_4932.ftz ### 智人（H. sapiens）物理型蛋白质-蛋白质相互作用数据集 训练集：dataset_9606_9606_train_physical.tsv.gz 测试集：dataset_9606_9606_test_physical.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_9606_9606_physical.ftz ### 黑腹果蝇（D. melanogaster）物理型蛋白质-蛋白质相互作用数据集 训练集：dataset_7227_7227_train_physical.tsv.gz 测试集：dataset_7227_7227_test_physical.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_7227_7227_physical.ftz ### 酿酒酵母（S. cerevisiae）物理型蛋白质-蛋白质相互作用数据集 训练集：dataset_4932_4932_train_physical.tsv.gz 测试集：dataset_4932_4932_test_physical.tsv.gz 基于该训练集训练的fastText句子分类模型：ft_model_CoCoScore_pretrained_4932_4932_physical.ftz ## 预训练词嵌入 预训练fastText词嵌入文件可从以下路径获取：fasttext_sg_masked_dim_300_epoch_5_lr_0.05_minn_3_maxn_6_ws_5.vec.gz