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An unprecedented number of crystallography database entries are undergoing extra checks amid fears that they are based on fabricated data. An unprecedented number of crystallography database entries are undergoing extra checks amid fears that they are based on fabricated data. Credit: Patrick McCabe/Alamy Exterior of the Cambridge Crystallographic Data Centre building.

The presented Bayesian network Integrated Testing Strategy (ITS-3) for skin sensitization potency assessment is a decision support system for a risk assessor that provides quantitative weight of evidence, leading to a mechanistically interpretable potency hypothesis, and formulates adaptive testing strategy for a chemical. The system was constructed with an aim to improve precision and accuracy for predicting LLNA potency beyond ITS-2 (Jaworska et al., J Appl Toxicol 33(11):1353–1364, 2013 ) by improving representation of chemistry and biology. Among novel elements are corrections for bioavailability both in vivo and in vitro as well as consideration of the individual assays’ applicability domains in the prediction process. In ITS-3 structure, three validated alternative assays, DPRA, KeratinoSens and h-CLAT, represent first three key events of the adverse outcome pathway for skin sensitization. The skin sensitization potency prediction is provided as a probability distribution over four potency classes. The probability distribution is converted to Bayes factors to: 1) remove prediction bias introduced by the training set potency distribution and 2) express uncertainty in a quantitative manner, allowing transparent and consistent criteria to accept a prediction. The novel ITS-3 database includes 207 chemicals with a full set of in vivo and in vitro data. The accuracy for predicting LLNA outcomes on the external test set ( n  = 60) was as follows: hazard (two classes)—100 %, GHS potency classification (three classes)—96 %, potency (four classes)—89 %. This work demonstrates that skin sensitization potency prediction based on data from three key events, and often less, is possible, reliable over broad chemical classes and ready for practical applications.

GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of deposited 'living' data sets. The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu ), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

The Molecule of the Month website (http://www.chm.bris.ac.uk/motm/motm.htm) is an educational resource that is celebrating its 20th anniversary. Here we reflect on its pioneering role in promoting new technology for visualizing and presenting chemical information on the web, as well as its achievements, as a free educational resource, both as a teaching aid and as a multi-user, multi-author learning platform. We discuss the legal aspects of such sites, as well as issues around how to make the content permanent. Finally, we look forward to how such sites may evolve in the future.

Giant database shows promise for replacing animal studies. Toxicologists this week unveiled a chemical safety screening tool that could greatly reduce the need for six common animal tests. Those tests account for nearly 60% of the estimated 3 million to 4 million animals used annually in risk testing worldwide. The computerized tool—built on a massive database of molecular structures and existing safety data—appears to match, and sometimes improve on, the results of animal tests for properties such as skin sensitization and eye irritation, the researchers report in today's issue of Toxicological Sciences . But it also has limitations; for instance, the method can't reliably evaluate a chemical's risk of causing cancer. And it's not clear how open regulatory agencies will be to adopting a nonanimal approach, although both European and U.S. regulators say they are open to the idea. Still, the big data approach is encouraging to those seeking to reduce and replace animal testing.

As plastic marine debris continues to accumulate in the oceans, many important questions surround this global dilemma. In particular, how many descriptors would be necessary to model the degradation behavior of ocean plastics or understand if degradation is possible? Here, we report a data-driven approach to elucidate degradation trends of plastic debris by linking abiotic and biotic degradation behavior in seawater with physical properties and molecular structures. The results reveal a hierarchy of predictors to quantify surface erosion as well as combinations of features, like glass transition temperature and hydrophobicity, to classify ocean plastics into fast, medium, and slow degradation categories. Furthermore, to account for weathering and environmental factors, two equations model the influence of seawater temperature and mechanical forces. Accumulation of micro and nano-plastic in the oceans has emerged as a global challenge. Here, the authors predict a hierarchy of features that regulate their degradation and surface erosion by a thorough analysis of polymer structure, composition, physical properties and degradation data.

Abstract BACKGROUND Plasma amino acid (PAA) profiles are used in routine clinical practice for the diagnosis and monitoring of inherited disorders of amino acid metabolism, organic acidemias, and urea cycle defects. Interpretation of PAA profiles is complex and requires substantial training and expertise to perform. Given previous demonstrations of the ability of machine learning (ML) algorithms to interpret complex clinical biochemistry data, we sought to determine if ML-derived classifiers could interpret PAA profiles with high predictive performance. METHODS We collected PAA profiling data routinely performed within a clinical biochemistry laboratory (2084 profiles) and developed decision support classifiers with several ML algorithms. We tested the generalization performance of each classifier using a nested cross-validation (CV) procedure and examined the effect of various subsampling, feature selection, and ensemble learning strategies. RESULTS The classifiers demonstrated excellent predictive performance, with the 3 ML algorithms tested producing comparable results. The best-performing ensemble binary classifier achieved a mean precision-recall (PR) AUC of 0.957 (95% CI 0.952, 0.962) and the best-performing ensemble multiclass classifier achieved a mean F4 score of 0.788 (0.773, 0.803). CONCLUSIONS This work builds upon previous demonstrations of the utility of ML-derived decision support tools in clinical biochemistry laboratories. Our findings suggest that, pending additional validation studies, such tools could potentially be used in routine clinical practice to streamline and aid the interpretation of PAA profiles. This would be particularly useful in laboratories with limited resources and large workloads. We provide the necessary code for other laboratories to develop their own decision support tools.

Since the first approval of a protein kinase inhibitor (PKI) by the Food and Drug Administration (FDA) in 2001, 55 new PKIs have reached the market, and many inhibitors are currently being evaluated in clinical trials. This is a clear indication that protein kinases still represent major drug targets for the pharmaceutical industry. In a previous work, we have introduced PKIDB, a publicly available database, gathering PKIs that have already been approved (Phase 4), as well as those currently in clinical trials (Phases 0 to 3). This database is updated frequently, and an analysis of the new data is presented here. In addition, we compared the set of PKIs present in PKIDB with the PKIs in early preclinical studies found in ChEMBL, the largest publicly available chemical database. For each dataset, the distribution of physicochemical descriptors related to drug-likeness is presented. From these results, updated guidelines to prioritize compounds for targeting protein kinases are proposed. The results of a principal component analysis (PCA) show that the PKIDB dataset is fully encompassed within all PKIs found in the public database. This observation is reinforced by a principal moments of inertia (PMI) analysis of all molecules. Interestingly, we notice that PKIs in clinical trials tend to explore new 3D chemical space. While a great majority of PKIs is located on the area of “flatland”, we find few compounds exploring the 3D structural space. Finally, a scaffold diversity analysis of the two datasets, based on frequency counts was performed. The results give insight into the chemical space of PKIs, and can guide researchers to reach out new unexplored areas. PKIDB is freely accessible from the following website: http://www.icoa.fr/pkidb.

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.