From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions

Ruusmann V.; Maran U.

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From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions

机译：从数据点时间表到精心挑选的数据集，从科学文章，问题和可能的解决方案中挖掘实验数据和化学结构数据的数据

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The scientific literature is important source of experimental and chemical structure data. Very often this data has been harvested into smaller or bigger data collections leaving the data quality and curation issues on shoulders of users. The current research presents a systematic and reproducible workflow for collecting series of data points from scientific literature and assembling a database that is suitable for the purposes of high quality modelling and decision support. The quality assurance aspect of the workflow is concerned with the curation of both chemical structures and associated toxicity values at (1) single data point level and (2) collection of data points level. The assembly of a database employs a novel "timeline" approach. The workflow is implemented as a software solution and its applicability is demonstrated on the example of the Tetrahymena pyriformis acute aquatic toxicity endpoint. A literature collection of 86 primary publications for T. pyriformis was found to contain 2,072 chemical compounds and 2,498 unique toxicity values, which divide into 2,440 numerical and 58 textual values. Every chemical compound was assigned to a preferred toxicity value. Examples for most common chemical and toxicological data curation scenarios are discussed.

机译：科学文献是实验和化学结构数据的重要来源。很多时候，这些数据已被收集到较小或较大的数据集中，而数据质量和策展问题则由用户承担。当前的研究提出了一种系统的，可重现的工作流程，用于从科学文献中收集一系列数据点，并组装一个适合于高质量建模和决策支持目的的数据库。工作流程的质量保证方面与（1）单个数据点级别和（2）数据点级别集合的化学结构和相关毒性值的管理有关。数据库的组装采用新颖的“时间轴”方法。该工作流以软件解决方案的形式实现，其适用性在梨形四膜虫急性水生毒性终点实例上得到了证明。我们发现86篇关于梨形毛霉的主要出版物的文献资料集包含2,072种化合物和2,498种独特的毒性值，这些毒性值分为2,440个数字值和58个文本值。将每种化合物指定为首选毒性值。讨论了最常见的化学和毒理学数据管理方案的示例。

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《Journal of Computer-Aided Molecular Design》 |2013年第7期|共21页
作者
Ruusmann V.; Maran U.;
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原文格式 PDF
正文语种 eng
中图分类 54.156;
关键词
Data curation; Data timelines; QSAR; Tetrahymena pyriformis; Toxicity data;

机译：数据管理;数据时间表;QSAR;梨形四膜虫;毒性数据;

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1. From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions [J] . Ruusmann V., Maran U. Journal of Computer-Aided Molecular Design . 2013,第7期

机译：从数据点时间表到精心挑选的数据集，从科学文章，问题和可能的解决方案中挖掘实验数据和化学结构数据的数据
2. Chemical structure and correlation analysis of HIV-1 NNRT and NRT inhibitors and database-curated, published inhibition constants with chemical structure in diverse datasets [J] . Viira Birgit, Garcia-Sosa Alfonso T., Maran Uko Journal of molecular graphics & modelling . 2017,第期

机译：HIV-1 NNRT和NRT抑制剂和数据库策划的化学结构和相关性分析，具有不同数据集中化学结构的公开抑制常数
3. Manually Curated Database of Rice Proteins (MCDRP), a database of digitized experimental data on rice ☆ [J] . Saurabh Raghuvanshi, Pratibha Gour, Shaji V. Joseph Current Plant Biology . 2016,第Volumesa7a8期

机译：人工管理的水稻蛋白数据库（MCDRP），有关水稻的数字化实验数据的数据库☆
4. Timeline and episode-structured clinical data: Pre-processing for Data Mining and analytics [C] . Jing Lu, Alan Hales, David Rew, 2016 IEEE 32nd International Conference on data Engineering Workshops . 2016

机译：时间轴和情节结构化的临床数据：数据挖掘和分析的预处理
5. Privacy preserving data mining using unrealized data sets -- Scope expansion and data compression. [D] . Fong, Pui Kuen. 2013

机译：使用未实现的数据集保护隐私的数据挖掘-范围扩展和数据压缩。
6. CPAD Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation [O] . A. Mary Thangakani, R. Nagarajan, Sandeep Kumar, -1

机译：CPAD固化蛋白聚集数据库：关于蛋白质和肽聚集的手动固化实验数据的存储库
7. Scientific journal «Plant and Soil Science» Font Size Make font size smaller Make font size default Make font size larger Language Select Language User Username Password Remember me Article Tools Print this article Indexing metadata How to cite item Finding References Email this article (Login required) Email the author (Login required) About The Authors YE. Krestʹyaninov National University of Life and Enviromental Sciences of Ukraine L. Yermakova National University of Life and Enviromental Sciences of Ukraine T. Antal National University of Life and Enviromental Sciences of Ukraine Social networks Information For Readers For Authors For Librarians Author Fees This journal charges the following author fees. Publication of one page: 50.00 (UAH) The fee include those of the journal’s publishing, online hosting and archiving. The ability of authors to pay the fee does not influence the peer review process. No fee can be paid prior to the final positive decision of the reviewers and the editor in charge, regarding the article proposed to be evaluated in order to be published. Depending upon each particular case, the fee can be covered by the journal edition. Details Recipient: National University of Life and Environmental Sciences of Ukraine Address: Heroyiv Oborony st., 15, Kyiv-03041, Ukraine. Current account number 31254247216289 Bank: State Treasury Service of Ukraine, Kyiv Bank code 820172 Certificate of VAT №100155865 Payment: In an article in scientific journal "Plant and Soil Science" Personal Account 18.02.06.06.01 Tel .: +38 044 527 87 20 Email: nti_dep@nubip.edu.ua Example of bibliographic description The list of journals included in scientometric databases: - Scopus (Uкraine, Belarus, Poland, Russia); - Іndex Copernicus; - Web of Sciense (humanities, natural sciences, social sciences); - РІНЦ. Search algorithm and calculation scientometric indicator: - Scopus; - Publish or Perish; - Google Scholar; - SNIP-іndex journal. Home About Login Register Search Current Archives Statistics Reminder for authors Editorial Board Home > Vol 10, No 1 (2019) > Krestʹyaninov Formation of corn grain yield and quality depending on micronutrients topdressing under conditions of Left bank Forest Steppe [O] . YE. Krestʹyaninov, L. Yermakova, T. Antal 2019

机译：科学杂志«植物和土壤科学»字体大小使字体大小较小Make Font Size默认制作字体大小较大语言选择语言用户用户用户用户用户用户名称打印本文索引项目查找参考文章查找参考文章电子邮件本文（需要登录）通过电子邮件发送给作者ye的作者（需要登录）。 Krest'yaninov国立生活大学L. Yermakova国立生活大学L. Yermakova国立生命大学乌克兰塔斯坦国立生命学院与乌克兰读者的环境网络社会网络信息图书馆员的社交网络信息作者作者费用的作者提供费用以下内容作者费用。出版一页：50.00（UAH）费用包括期刊出版，在线托管和归档的费用。作者支付费用的能力不会影响同行评审过程。在审核人员和负责编辑的最终决定之前，无需支付费用，就拟议的文章进行了评估，以便公布。根据每个特定案例，期刊版本可以涵盖费用。详细资料收件人：国立生活大学乌克兰的环境科学地址：伊莱夫·奥诺齐St.，15，Kyiv-03041，乌克兰。当前账户号码31254247216289银行：乌克兰国家财政部服务，基辅银行代码820172增值税证书№100155865付款：在科学期刊“植物和土壤科学”个人账户中的一篇文章18.02.06.06.01电话。：+38 044 527 87 20封电子邮件：nti_dep@nubip.edu.ua书目描述的示例，Sciporal数据库中包含的期刊列表： - Scopus（uкraine，白俄罗斯，波兰，俄罗斯）; - іdex哥白尼; - 巩膜网（人文，自然科学，社会科学）; - рінц。搜索算法与计算科学计量指标： - Scopus; - 发表或灭亡; - 谷歌学术; - Snip-index杂志。主页关于登录登记搜索当前档案统计提醒为作者编辑委员会主页> Vol 10，第1（2019）> Krest'yaninov在左岸森林草原条件下的微量营养营养营养营养品，质量

From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions

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