Inferring Ontological Categories of OWL Classes Using Foundational Rules

Several efforts that leverage the tools of formal ontology (such as OntoClean, OntoUML, and UFO) have demonstrated the fruitfulness of considering key metaproperties of classes in ontology engineering. These metaproperties include sortality, rigidity, and external dependence, and give rise to many fine-grained ontological categories for classes, including, among others, kinds, phases, roles, mixins, etc. Despite that, it is still common practice to apply representation schemes and approaches - such as OWL - that do not benefit from identifying these ontological categories, and simplistically treat all classes in the same manner. In this paper, we propose an approach to support the automated classification of classes into the ontological categories underlying the (g)UFO foundational ontology. We propose a set of inference rules derived from (g)UFO's axiomatization that, given an initial classification of the classes in an OWL ontology, can support the inference of the classification for the remaining classes in the ontology. We formalize these rules, implement them in a computational tool and assess them against a catalog of ontologies designed by a variety of users for a number of domains.</p

Boosting D3FEND: Ontological Analysis and Recommendations

Formal Ontology is a discipline whose business is to develop formal theories about general aspects of reality such as identity, dependence, parthood, truthmaking, causality, etc. A foundational ontology is a specific consistent set of these ontological theories that support activities such as domain analysis, conceptual clarification, and meaning negotiation. A (well-founded) core ontology specifies, under a foundational ontology, the central concepts and relations of a given domain. Foundational and core ontologies can be seen as ontology engineering frameworks to systematically address the laborious task of building large (more specific) domain ontologies. However, both in research and industry, it is common that ontologies as computational artifacts are built without the aid of any framework of this kind, favoring the occurrence of numerous modeling mistakes and gaps. Through a case study, here we show an exemplar of such a case in the domain of cybersecurity by providing an ontological analysis of D3FEND, an OWL knowledge graph of cybersecurity countermeasure techniques proposed by the MITRE Corporation. Based on the Reference Ontology for Security Engineering (ROSE), a core ontology of the security domain founded in the Unified Foundational Ontology (UFO), our investigation reveals a number of semantic deficiencies in D3FEND, including missing concepts, semantic overload of terms, and a systematic lack of constraints that renders that model under-specified. As a result of our ontological analysis, we propose several suggestions for the appropriate redesign of D3FEND to overcome those issues.</p

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

A FAIR Model Catalog for Ontology-Driven Conceptual Modeling Research

Conceptual models are artifacts representing conceptualizations of particular domains. Hence, multi-domain model catalogs serve as empirical sources of knowledge and insights about specific domains, about the use of a modeling language’s constructs, as well as about the patterns and anti-patterns recurrent in the models of that language crosscutting different domains. However, to support domain and language learning, model reuse, knowledge discovery for humans, and reliable automated processing and analysis by machines, these catalogs must be built following generally accepted quality requirements for scientific data management. Especially, all scientific (meta)data—including models—should be created using the FAIR principles (Findability, Accessibility, Interoperability, and Reusability). In this paper, we report on the construction of a FAIR model catalog for Ontology-Driven Conceptual Modeling research, a trending paradigm lying at the intersection of conceptual modeling and ontology engineering in which the Unified Foundational Ontology (UFO) and OntoUML emerged among the most adopted technologies. In this initial release, the catalog includes over a hundred models, developed in a variety of contexts and domains. The paper also discusses the research implications for (ontology-driven) conceptual modeling of such a resource