Journal of Computer-Aided Molecular Design

, Volume 27, Issue 7, pp 583–603 | Cite as

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

  • Villu Ruusmann
  • Uko Maran


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.


Data curation Data timelines Toxicity data Tetrahymena pyriformis QSAR 



Estonian Science Foundation (Grant 7709) and Estonian Ministry for Education and Research (Grant SF0140031Bs09) for financial support. Authors are grateful to Prof. T.W. Schultz (University of Tennessee) for his assistance in resolving selected data points. Authors are thankful to Dr. Sulev Sild (University of Tartu, Estonia) for the discussion at final stages of manuscript preparation.

Supplementary material

10822_2013_9664_MOESM1_ESM.doc (612 kb)
Supplementary Material includes Tables with examples for data curation with respective detailed discussion and fully curated dataset. (DOC 612 kb)
10822_2013_9664_MOESM2_ESM.xls (737 kb)
Supplementary material 2 (XLS 737 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Institute of ChemistryUniversity of TartuTartuEstonia

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