Cancermine

This describes the output files for the CancerMine project. These files are loaded directly by the CancerMine viewer. The code for this viewer is available in the CancerMine Github repo if you want to run it independently. Each file is a tab-delimited file with a header, no comments and no quoting. You likely want <strong>cancermine_collated.tsv</strong> if you just want the list of cancer gene roles. If you want the supporting sentences, look at <strong>cancermine_sentences.tsv</strong>. You can use the <em>matching_id</em> column to connect the two files. If you want to dig further and are okay with a higher false positive rate, look at <strong>cancermine_unfiltered.tsv</strong>. <strong>cancermine_collated.tsv:</strong> This contains the cancer gene roles with citation counts supporting them. It contains the normalized cancer and gene names along with IDs for HUGO, Entrez Gene and the Disease Ontology. <strong>cancermine_sentences.tsv:</strong> This contains the supporting sentences for the cancer gene roles in the collated file. Each row is a single supporting sentence for one cancer gene role. This file contains information on the source publication (e.g. journal, publication date, etc), the actual sentence and the cancer gene role extracted. <strong>cancermine_unfiltered.tsv:</strong> This is the raw output of the applyModelsToSentences.py script across all of PubMed, Pubmed Central Open Access and PubMed Central Author Manuscript Collection. It contains every predicted relation with a prediction score above 0.5. So this may contain many false positives. Each row contain information on the publication (e.g. journal, publication date, etc) along with the sentence and the specific cancer gene role extracted (with HUGO, Entrez Gene and Disease Ontology IDs). This file is further processed to create the other two.本说明针对CancerMine项目的输出文件展开。此类文件可直接加载至CancerMine浏览器中运行。若您希望独立部署该浏览器，其代码可于CancerMine的GitHub仓库中获取。所有文件均为带表头的制表符分隔值（Tab-Separated Values，TSV）文件，无注释行，亦未使用引号包裹内容。 若您仅需获取癌症基因作用关系列表，推荐使用**cancermine_collated.tsv**。若需查看支撑该关系的文献语句，请查阅**cancermine_sentences.tsv**，可通过`matching_id`字段实现两份文件的关联匹配。若您希望进一步探索且可接受较高的假阳性率，则可参考**cancermine_unfiltered.tsv**。 **cancermine_collated.tsv**：该文件收录了带有引用计数的癌症基因作用关系，包含标准化后的癌症与基因名称，以及HUGO（人类基因组组织）、Entrez Gene与疾病本体论(Disease Ontology)的对应标识符。 **cancermine_sentences.tsv**：该文件包含汇总文件中癌症基因作用关系的支撑性文献语句。每一行对应单条癌症基因作用关系的单条支撑语句，涵盖来源出版物的相关信息（如期刊、发表日期等）、原文语句以及提取得到的癌症基因作用关系条目。 **cancermine_unfiltered.tsv**：该文件为`applyModelsToSentences.py`脚本在覆盖全部PubMed、PubMed Central开放获取合集与PubMed Central作者手稿合集的所有文献上运行后的原始输出结果，收录了所有预测评分高于0.5的关联关系，因此可能包含大量假阳性样本。每一行均包含出版物相关信息（如期刊、发表日期等）、原文语句以及提取得到的具体癌症基因作用关系条目（附带HUGO、Entrez Gene与疾病本体论(Disease Ontology)标识）。后续另外两份文件均由该文件进一步处理得到。