The COVID-19 Ontology.

MOTIVATION: The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development. RESULTS: The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute. AVAILABILITYAND IMPLEMENTATION: COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Neurosymbolic AI for Reasoning Over Knowledge Graphs: A Survey.

Neurosymbolic artificial intelligence (AI) is an increasingly active area of research that combines symbolic reasoning methods with deep learning to leverage their complementary benefits. As knowledge graphs (KGs) are becoming a popular way to represent heterogeneous and multirelational data, methods for reasoning on graph structures have attempted to follow this neurosymbolic paradigm. Traditionally, such approaches have utilized either rule-based inference or generated representative numerical embeddings from which patterns could be extracted. However, several recent studies have attempted to bridge this dichotomy to generate models that facilitate interpretability, maintain competitive performance, and integrate expert knowledge. Therefore, we survey methods that perform neurosymbolic reasoning tasks on KGs and propose a novel taxonomy by which we can classify them. Specifically, we propose three major categories: 1) logically informed embedding approaches; 2) embedding approaches with logical constraints; and 3) rule-learning approaches. Alongside the taxonomy, we provide a tabular overview of the approaches and links to their source code, if available, for more direct comparison. Finally, we discuss the unique characteristics and limitations of these methods and then propose several prospective directions toward which this field of research could evolve.

MultiGML: Multimodal graph machine learning for prediction of adverse drug events.

Adverse drug events constitute a major challenge for the success of clinical trials. Several computational strategies have been suggested to estimate the risk of adverse drug events in preclinical drug development. While these approaches have demonstrated high utility in practice, they are at the same time limited to specific information sources. Thus, many current computational approaches neglect a wealth of information which results from the integration of different data sources, such as biological protein function, gene expression, chemical compound structure, cell-based imaging and others. In this work we propose an integrative and explainable multi-modal Graph Machine Learning approach (MultiGML), which fuses knowledge graphs with multiple further data modalities to predict drug related adverse events and general drug target-phenotype associations. MultiGML demonstrates excellent prediction performance compared to alternative algorithms, including various traditional knowledge graph embedding techniques. MultiGML distinguishes itself from alternative techniques by providing in-depth explanations of model predictions, which point towards biological mechanisms associated with predictions of an adverse drug event. Hence, MultiGML could be a versatile tool to support decision making in preclinical drug development.

A machine learning method for the identification and characterization of novel COVID-19 drug targets.

In addition to vaccines, the World Health Organization sees novel medications as an urgent matter to fight the ongoing COVID-19 pandemic. One possible strategy is to identify target proteins, for which a perturbation by an existing compound is likely to benefit COVID-19 patients. In order to contribute to this effort, we present GuiltyTargets-COVID-19 ( https://guiltytargets-covid.eu/ ), a machine learning supported web tool to identify novel candidate drug targets. Using six bulk and three single cell RNA-Seq datasets, together with a lung tissue specific protein-protein interaction network, we demonstrate that GuiltyTargets-COVID-19 is capable of (i) prioritizing meaningful target candidates and assessing their druggability, (ii) unraveling their linkage to known disease mechanisms, (iii) mapping ligands from the ChEMBL database to the identified targets, and (iv) pointing out potential side effects in the case that the mapped ligands correspond to approved drugs. Our example analyses identified 4 potential drug targets from the datasets: AKT3 from both the bulk and single cell RNA-Seq data as well as AKT2, MLKL, and MAPK11 in the single cell experiments. Altogether, we believe that our web tool will facilitate future target identification and drug development for COVID-19, notably in a cell type and tissue specific manner.

Corrigendum to "Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases"[Artificial Intelligence in Life Sciences] 1(2021), 100020.

[This corrects the article DOI: 10.1016/j.ailsci.2021.100020.].

Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases.

Despite available vaccinations COVID-19 case numbers around the world are still growing, and effective medications against severe cases are lacking. In this work, we developed a machine learning model which predicts mortality for COVID-19 patients using data from the multi-center 'Lean European Open Survey on SARS-CoV-2-infected patients' (LEOSS) observational study (>100 active sites in Europe, primarily in Germany), resulting into an AUC of almost 80%. We showed that molecular mechanisms related to dementia, one of the relevant predictors in our model, intersect with those associated to COVID-19. Most notably, among these molecules was tyrosine kinase 2 (TYK2), a protein that has been patented as drug target in Alzheimer's Disease but also genetically associated with severe COVID-19 outcomes. We experimentally verified that anti-cancer drugs Sorafenib and Regorafenib showed a clear anti-cytopathic effect in Caco2 and VERO-E6 cells and can thus be regarded as potential treatments against COVID-19. Altogether, our work demonstrates that interpretation of machine learning based risk models can point towards drug targets and new treatment options, which are strongly needed for COVID-19.

A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.

The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific community's massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2/COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.