ArticleJournal of computer-aided molecular design2013
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.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- A Benchmark Study of Graph Models for Molecular Acute Toxicity Prediction.International journal of molecular sciences · 2023Article
- Article
- Intrinsic Aqueous Solubility: Mechanistically Transparent Data-Driven Modeling of Drug Substances.Pharmaceutics · 2022Article
- Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies.Frontiers in genetics · 2020Article
- The good, the bad, and the ugly in chemical and biological data for machine learning.Drug discovery today. Technologies · 2019Article
- Best Practices for QSAR Model Reporting: Physical and Chemical Properties, Ecotoxicity, Environmental Fate, Human Health, and Toxicokinetics Endpoints.Environmental health perspectives · 2018Review
- Article
- QSAR DataBank repository: open and linked qualitative and quantitative structure-activity relationship models.Journal of cheminformatics · 2015Article
- QSAR DataBank - an approach for the digital organization and archiving of QSAR model information.Journal of cheminformatics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Indexed as
Identifiers
23884706What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.