When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies

In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous 'FOWL' ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level ontology BFO via our approach enables us to detect several inconsistencies. Furthermore, existing OWL ontologies can benefit from FOL annotations. We illustrate this with FOWL ontologies containing mereotopological axioms that enable new meaningful inferences. Finally, we show that even for large domain ontologies such as ChEBI, automatic reasoning with FOL annotations can be used to detect previously unnoticed errors in the classification

Ontology Pre-training for Poison Prediction

Integrating human knowledge into neural networks has the potential to improve their robustness and interpretability. We have developed a novel approach to integrate knowledge from ontologies into the structure of a Transformer network which we call ontology pre-training: we train the network to predict membership in ontology classes as a way to embed the structure of the ontology into the network, and subsequently fine-tune the network for the particular prediction task. We apply this approach to a case study in predicting the potential toxicity of a small molecule based on its molecular structure, a challenging task for machine learning in life sciences chemistry. Our approach improves on the state of the art, and moreover has several additional benefits. First, we are able to show that the model learns to focus attention on more meaningful chemical groups when making predictions with ontology pre-training than without, paving a path towards greater robustness and interpretability. Second, the training time is reduced after ontology pre-training, indicating that the model is better placed to learn what matters for toxicity prediction with the ontology pre-training than without. This strategy has general applicability as a neuro-symbolic approach to embed meaningful semantics into neural networks

Predicting outcomes of smoking cessation interventions in novel scenarios using ontology-informed, interpretable machine learning

Background Systematic reviews of effectiveness estimate the relative average effects of interventions and comparators in a set of existing studies e.g., using rate ratios. However, policymakers, planners and practitioners require predictions about outcomes in novel scenarios where aspects of the interventions, populations or settings may differ. This study aimed to develop and evaluate an ontology-informed, interpretable machine learning algorithm to predict smoking cessation outcomes using detailed information about interventions, their contexts and evaluation study methods. This is the second of two linked papers on the use of machine learning in the Human Behaviour-Change Project. Methods The study used a corpus of 405 reports of randomised trials of smoking cessation interventions from the Cochrane Library database. These were annotated using the Behaviour Change Intervention Ontology to classify, for each of 971 study arms, 82 features representing details of intervention content and delivery, population, setting, outcome, and study methodology. The annotated data was used to train a novel machine learning algorithm based on a set of interpretable rules organised according to the ontology. The algorithm was evaluated for predictive accuracy by performance in five-fold 80:20 cross-validation, and compared with other approaches. Results The machine learning algorithm produced a mean absolute error in prediction percentage cessation rates of 9.15% in cross-validation, outperforming other approaches including an uninterpretable ‘black-box’ deep neural network (9.42%), a linear regression model (10.55%) and a decision tree-based approach (9.53%). The rules generated by the algorithm were synthesised into a consensus rule set to create a publicly available predictive tool to provide outcome predictions and explanations in the form of rules expressed in terms of predictive features and their combinations. Conclusions An ontologically-informed, interpretable machine learning algorithm, using information about intervention scenarios from reports of smoking cessation trials, can predict outcomes in new smoking cessation intervention scenarios with moderate accuracy.</ns3:p

Identification of user requirements for an energy scenario database

Energy scenarios assist decision making regarding the transformation of the energy supply system. A multitude of scenarios exists in various formats. Thus, for scientists and policy stakeholders alike, it remains difficult to distinguish and compare scenario data. Hence, the aim of the project SzenarienDB is to establish an energy scenario database containing data in comparable and machine-readable format. SzenarienDB will do so by extending the OpenEnergyPlatform (OEP). To ensure that the extension fulfils the requirements of the modelling community, we conducted an online survey. We asked the participants about what they expected of an energy scenario database. Along with input from expert meetings and GitHub issues on that topic, we derived user requirement from the answers. In total, we identified 69 requirements. Out of these, around 44% were considered as very urgent. Hence, we conclude that there is a great need for the development of a consistent energy scenario database. To tackle the requirements we grouped these into twelve categories: input and output, data review process, bug-fixes, documentation, factsheets, features, functions to modify data, layout, metadata, ontology, references, and other. Each category is resolved according to its intrinsic properties

Pet Rodents and Fatal Lymphocytic Choriomeningitis in Transplant Patients

A unique strain of this virus was traced back to hamsters from an Ohio rodent distribution facility

Introduction and evaluation of the Open Energy Ontology (OEO)

See attached fil

Introducing the Open Energy Ontology: Enhancing data interpretation and interfacing in energy systems analysis

Heterogeneous data, different definitions and incompatible models are a huge problem in many domains, with no exception for the field of energy systems analysis. Hence, it is hard to re-use results, compare model results or couple models at all. Ontologies provide a precisely defined vocabulary to build a common and shared conceptualisation of the energy domain. Here, we present the Open Energy Ontology (OEO) developed for the domain of energy systems analysis. Using the OEO provides several benefits for the community. First, it enables consistent annotation of large amounts of data from various research projects. One example is the Open Energy Platform (OEP). Adding such annotations makes data semantically searchable, exchangeable, re-usable and interoperable. Second, computational model coupling becomes much easier. The advantages of using an ontology such as the OEO are demonstrated with three use cases: data representation, data annotation and interface homogenisation. We also describe how the ontology can be used for linked open data (LOD)