PretoxTM Corpus: a gold standard corpus of preclinical treatment-related findings annotated from toxicology reports

The PretoxTM Corpus is a gold standard corpus of preclinical treatment-related findings annotated from toxicology reports. Example documents annotated by domain experts, also known as a gold standard corpus, are needed in order to develop, train, and validate text mining tools. To this aim we designed and performed an annotation activity for the development of the corpus of treatment-related findings: the PretoxTM corpus. A treatment-related finding expression enclose several named entities; the most relevant one is the abnormal effect detected; which depending on the study domain of the finding, can be given by a measurement, test, or examination named Study Test and an abnormal Manifestation result obtained for that study test; or by an abnormal Finding in study domains where there is no associated test or measurement (e.g., clinical, macroscopic and microscopic). Other related named entities that could be present to complete the treatment-related finding are; the Specimen of the abnormal observation, the Sex of the subject, the Group of subjects in which the observation was detected and the Dose level administration of the compound. Examples of sentences with treatment-related findings are: “The decrease in food consumption and body weight of the animals from the mid dose onwards is regarded as evidence of general toxicity.” and "At dose level 3, absolute and relative liver weights were increased in male rats.”. Contributions: The PretoxTM corpus was developed by BSC, with the contribution of IMIM and a team of experts from the eTRANSAFE EFPIA partners. License: Creative Commons Attribution-ShareAlike 4.0 International (cc by sa 4.0). The PretoxTM resources have been developed as part of the eTRANSAFE project. For more information about PretoxTM please visit: PretoxTM Corpus Gitlab: https://gitlab.bsc.es/inb/etransafe/preclinical-toxicological-corpus/ PretoxTM central documentation: https://pretoxtm.gitlab.io/documentation/PretoxTM语料库是一套从毒理学报告中标注得到的、面向临床前治疗相关发现的金标准语料库。 由领域专家标注的示例文档（即金标准语料库）是开发、训练与验证文本挖掘工具的必要支撑。为此，我们针对治疗相关发现语料库的构建开展了标注工作，即本研究中的PretoxTM语料库。 治疗相关发现表述包含多个命名实体，其中最核心的为检测到的异常效应。根据发现所属的研究领域，该异常效应可通过两类形式体现：其一为以研究试验（Study Test）为标识的检测、检验或测量手段，以及对应该试验得到的异常表现（Manifestation）结果；其二为无关联检测或测量手段的研究领域中的异常发现（例如临床、大体与微观领域）。用于完整描述治疗相关发现的其他相关命名实体还包括：异常观察的样本（Specimen）、受试对象的性别、观察到异常的受试对象组别，以及受试化合物的给药剂量水平。包含治疗相关发现的例句如下："中剂量及以上给药组动物的食物摄入量与体重下降，被认定为全身毒性的佐证。"以及"在剂量水平3下，雄性大鼠的绝对与相对肝脏重量均出现升高。" 贡献说明：PretoxTM语料库由BSC主导开发，同时得到了IMIM与eTRANSAFE EFPIA合作方专家团队的参与贡献。 许可协议：知识共享署名-相同方式共享4.0国际版（CC BY-SA 4.0）。 PretoxTM相关资源作为eTRANSAFE项目的一部分开发完成。 如需了解PretoxTM的更多信息，请访问： PretoxTM语料库Gitlab仓库：https://gitlab.bsc.es/inb/etransafe/preclinical-toxicological-corpus/ PretoxTM核心文档：https://pretoxtm.gitlab.io/documentation/