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Critical minerals are increasingly used in advanced, modern technologies. Exploration for these minerals require efficient mechanisms to search for the latest geological knowledge about the petrogenesis and spatial distribution of these essential resources. Although the current text-based deposit classification schemes help geoscientists to understand how and where these critical minerals form, they cannot easily be queried by software without extensive natural language processing and knowledge modeling. Ontologies can explicitly specify the knowledge scattered in the texts and tables of these schemes and the Critical Minerals Mapping Initiative (CMMI) database by way of logical structures whose results can automatically be processed and queried. They can also draw new knowledge by inference from the ones that are explicitly specified in them. These qualities make ontologies a perfect choice for digital knowledge storage, search, and extraction. The Critical Minerals Ontology (CMO) is described herein by reusing the logical class and property structures of the top-level Basic Formal Ontology (BFO) and mid-level Common Core Ontologies (CCO) and Relation Ontology (RO). The CMO formally models the knowledge about the critical mineral systems using the latest deposit classification scheme and the CMMI database schema. The ontology specifies the geochemical and geological processes that operate in various geotectonic environments of mineral systems to form the critical minerals in different deposit types. It models the properties of both the host minerals that contain the rare-earth elements and those that bear other types of elements. The CMO also represents uses of specific critical minerals in the manufacturing of industrial products, their alternate substitutes, and countries that produce, import, and export them. A query system, applying the Python programming language, accesses the knowledge modeled in the CMO and allows users through interactive web pages to query the ontology and extract different types of information from it. The ontology and the query system are useful for research in ore mineralogy and critical mineral prospecting. The information modeled by the ontology and served by the query system allows users to classify their ore specimen data into specific deposit types.

In a proof of concept study, we assessed the feasibility of designing a first-order logic (FOL) framework capable of translating SNOMED CT's terminological view on patient data as referencing concepts, into the realism-based view of the Basic Formal Ontology and the Ontology for General Medical Science according to which patient data represent instances of types. Because within the subject domain of this study, SNOMED CT's terminological coverage was excellent, and its EL++ axioms can be automatically translated into FOL as well as the antecedent part of bridging axioms between SNOMED CT and realism-based ontologies, we conclude that this is an area of R&D that deserves further attention and that may lead to new ways of federating terminologies with ontologies. [ABSTRACT FROM AUTHOR]

The construction industry produces enormous amounts of information, relying on building information modeling (BIM). However, due to interoperability issues, valuable information is not being used properly. Ontology offers a solution to this interoperability. A complete knowledge base can be provided by reusing basic formal ontology (BFO). In previous studies, domain ontology was developed without BFO. Domain ontology requires loads of effort to reuse because domain ontology is too detailed. To increase the reuse rate and establish a complete knowledge base, it is necessary to develop BFO. This study has developed the BFO in the BIM domain to advance interoperability. First, unnecessary parts were omitted from the existing BFO development process, the process was simplified, and the base of hierarchy was created by extracting the most basic superclasses of the BFO model from Revit, the software of BIM. Based on that hierarchy, each child class was created, and the BFO model was completed by completing the relation of each class. After completion of the model, reliability, in addition to the completeness of the model, was evaluated through a query. Domain experts can reuse the BFO when defining relations between concepts and entities. The proposed BFO will be the foundation of future ontology developments in the BIM domain. This study facilitates future researchers to enhance interoperability in the BIM domain and make the ontology more complete to improve information sharing. [ABSTRACT FROM AUTHOR]

Alzheimer's disease is a debilitating neurodegenerative condition which is known to be the most common cause of dementia. Despite its rapidly growing prevalence, medicine still lacks a comprehensive definition of the disease. As a result, Alzheimer's disease remains neither preventable nor curable. In recent years, broad interdisciplinary collaborations in Alzheimer's disease research are becoming more common. Furthermore, such collaborations have already demonstrated their superiority in addressing the complexity of the disease in innovative ways. However, establishing effective communication and optimal knowledge distribution between researchers and specialists with different expertise and background is not a straightforward task. To address this challenge, we propose the Alzheimer's disease Ontology for Diagnosis and Preclinical Classification (AD-DPC) as a tool for effective knowledge sharing in interdisciplinary/multidisciplinary teams working on Alzheimer's disease. It covers six major conceptual groups, namely Alzheimer's disease pathology, Alzheimer's disease spectrum, Diagnostic process, Symptoms, Assessments, and Relevant clinical findings. All concepts were annotated with definitions or elucidations and in some cases enriched with synonyms and additional resources. The potential of AD-DPC to support non-medical experts is demonstrated through an evaluation of its usability, applicability and correctness. The results show that the participants in the evaluation process who lack prior medical knowledge can successfully answer Alzheimer's disease-related questions by interacting with AD-DPC. Furthermore, their perceived level of knowledge in the field increased leading to effective communication with medical experts. [ABSTRACT FROM AUTHOR]

Objetivo: Descrever, com ontologia, a representação de documentos de acordo com os princípios e conceitos da Arquivologia. A análise ontológica teve enfoque na produção documental de uma organização, permitindo que ontologias desenvolvidas para organizações possam ser compatibilizadas com os princípios e soluções da Arquivologia, quando a questão é o documento e sua produção. Método: Análise ontológica de conceitos com enfoque na classificação de entidades arquivísticas nas classes especificadas na ontologia de alto nível Basic Formal Ontology (BFO) no que se refere a: informação, documento arquivístico e materialidade; produção de documento arquivístico; e contextos jurídico-administrativo, administrativo, documental e de proveniência. Resultado: O modelo ontológico esclarece e especifica o significado semântico dos conceitos arquivísticos analisados, construindo um suporte para derivações lógicas destes documentos, associação destes documentos com entidades que representam conteúdos de domínio especificadas em outras ontologias derivadas da BFO Conclusões: Os resultados demonstram que os conceitos arquivísticos estão alinhados à BFO em uma relação de subsunção com relação aos aspectos analisados. Se observa que o documento arquivístico é fundamentado pelas percepções de realidade de BFO.

The construction industry produces enormous amounts of information, relying on building information modeling (BIM). However, due to interoperability issues, valuable information is not being used properly. Ontology offers a solution to this interoperability. A complete knowledge base can be provided by reusing basic formal ontology (BFO). In previous studies, domain ontology was developed without BFO. Domain ontology requires loads of effort to reuse because domain ontology is too detailed. To increase the reuse rate and establish a complete knowledge base, it is necessary to develop BFO. This study has developed the BFO in the BIM domain to advance interoperability. First, unnecessary parts were omitted from the existing BFO development process, the process was simplified, and the base of hierarchy was created by extracting the most basic superclasses of the BFO model from Revit, the software of BIM. Based on that hierarchy, each child class was created, and the BFO model was completed by completing the relation of each class. After completion of the model, reliability, in addition to the completeness of the model, was evaluated through a query. Domain experts can reuse the BFO when defining relations between concepts and entities. The proposed BFO will be the foundation of future ontology developments in the BIM domain. This study facilitates future researchers to enhance interoperability in the BIM domain and make the ontology more complete to improve information sharing.

El artículo define las ontologías en el ámbito de la Web semántica, donde se las describe como artefactos representacionales, dispositivos jerárquicos constituidos por entidades y relaciones, y se las tipifica de acuerdo con su grado de generalidad y su funcionalidad. Se destacan los principios básicos que las rigen y las buenas prácticas a tener en cuenta a nivel lógico para su diseño e implementación de acuerdo con la Basic Formal Ontology (BFO), orientada a sustentar las cuestiones lógicas de todo tipo de ontologías. Esquematiza las clases que incluye BFO, sus relaciones y principales axiomas. Subraya el impacto de la expresividad de los lenguajes utilizados al diseñar ontologías en cuanto a la resolución de los aspectos formales que influyen en la capacidad de éstas para generar inferencias automáticamente.= The article defines the ontologies in the Semantic Web, where they are described as representational artifacts, hierarchical devices constituted by entities and relationships, and are typified according to their degree of generality and functionality. It highlights the basic principles that govern them and good practices to be taken into account at the logical level for their design and implementation in accordance with the Basic Formal Ontology (BFO) oriented to support the logical issues of all types of ontologies. It defines the classes that BFO includes, its relationships and main axioms. It emphasizes the impact of the expressiveness of the languages used when designing ontologies in terms of the resolution of formal aspects that influence the ability of these to generate inferences automatically.

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from the Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. [ABSTRACT FROM AUTHOR]

In this paper, we present a domain-specific, open access, reference ontology (ROMAIN) for the maintenance management domain. We use a hybrid approach, based on a top-down alignment to an open source top-level ontology, the Basic Formal Ontology (BFO), and a bottom up focus on classes that are grounded in maintenance practice. We constrain the scope of the ontology to the classes that are unique to the maintenance management practice, such as maintenance strategy, degradation, and work order management, rather than modeling the entire domain of maintenance. This approach reduces the scope of the development task and enables reasoning to be tested at a manageable scale. ROMAIN provides a unifying framework that can be used in conjunction with other BFO compliant sub-domain ontologies, such as planning and scheduling ontologies. The proposed ontology is validated using real-life data in the context of a use case related to evaluating the effectiveness of maintenance strategy. [ABSTRACT FROM AUTHOR]

The goal of implementing an enterprise digital engineering strategy is to improve data sharing throughout system conceptualization, development, manufacturing, operations, sustainment and their supporting organizations. Data sharing is a critical element of interoperability of models and other digital artifacts supporting the systems engineering process. Achieving interoperability within systems engineering requires eliminating differences of syntax and semantics to take advantage of automation, augmentation, and artificial intelligence capabilities that will increase process efficiency and artifact quality. This paper describes the development of a process-centric Systems Engineering (SE) reference ontology, based upon ISO/IEC/IEEE 15288 Systems and Software Engineering – Life Cycle Processes [1]. The proposed SE reference ontology extends from the Basic Formal Ontology (BFO), which is a very small top-level ontology (TLO) designed specifically to support the integration of more specific ontologies that extend from it [2]. A reference ontology is intended to provide a comprehensive representation of the entities in a given domain encapsulating the terminological content of established knowledge. Unlike other systems ontologies, which focus on the target systems, this reference ontology is focused on the systems engineering process, providing context and purpose for the digital artifacts being built and linking the content of artifacts together into one lexicon. [ABSTRACT FROM AUTHOR]

In a proof of concept study, we assessed the feasibility of designing a first-order logic (FOL) framework capable of translating SNOMED CT's terminological view on patient data as referencing concepts, into the realism-based view of the Basic Formal Ontology and the Ontology for General Medical Science according to which patient data represent instances of types. Because within the subject domain of this study, SNOMED CT's terminological coverage was excellent, and its EL++ axioms can be automatically translated into FOL as well as the antecedent part of bridging axioms between SNOMED CT and realism-based ontologies, we conclude that this is an area of R&D that deserves further attention and that may lead to new ways of federating terminologies with ontologies.

The Basic Formal Ontology (BFO) class continuant fiat boundary and its subclasses, including fiat surface , are not heavily axiomatized; they have elucidations, not definitions; and the meanings of these elucidations are poorly captured by the relevant BFO axioms. This paper is an effort to make progress in these respects for fiat surface . We identify a range of desiderata for a BFO-conformant view of fiat surface , argue that the GitHub does not satisfy them, argue that the view of fiat surfaces in Arp et al. (2015) does a better job, and supplement that view in ways that do a still better job. Our discussion allows us to, inter alia , present a number of axioms relevant to our topic worthy of consideration for inclusion in BFO or dependent ontologies in specific domains and for specific purposes.

Vector-borne diseases (VBDs) are a kind of infection caused through the transmission of vectors generated by the bites of infected parasites, bacteria, and viruses, such as ticks, mosquitoes, triatomine bugs, blackflies, and sandflies. If these diseases are not properly treated within a reasonable time frame, the mortality rate may rise. In this work, we propose a set of ontologies that will help in the diagnosis and treatment of vector-borne diseases. For developing VBD's ontology, electronic health records taken from the Indian Health Records website, text data generated from Indian government medical mobile applications, and doctors' prescribed handwritten notes of patients are used as input. This data is then converted into correct text using Optical Character Recognition (OCR) and a spelling checker after pre-processing. Natural Language Processing (NLP) is applied for entity extraction from text data for making Resource Description Framework (RDF) medical data with the help of the Patient Clinical Data (PCD) ontology. Afterwards, Basic Formal Ontology (BFO), National Vector Borne Disease Control Program (NVBDCP) guidelines, and RDF medical data are used to develop ontologies for VBDs, and Semantic Web Rule Language (SWRL) rules are applied for diagnosis and treatment. The developed ontology helps in the construction of decision support systems (DSS) for the NVBDCP to control these diseases. [ABSTRACT FROM AUTHOR]

A realist ontology of the modern human experience is built using the Basic Formal Ontology. Four measurable and observable entities are identified as upper-level and universal in the domain of human experience. All other entities and abstractions are shown to emerge from these. The universals are: material things, individual humans, money and energy. A four by four matrix of the universals creates ten phenomena-based categories that systematically map the domains codified in the Dewey Decimal Classification. The matrix is an example of the property of low-emergence in human development. A human research study using interview methodology linked the sufficiency of seven common instances of each universal to fully cover the subjective and present life experiences of twenty-five physically, educationally, economically and culturally diverse participants. To address the significant diversity of human experience, the universals and instances used in the human research are realistically mapped onto a Rubik's Cube. Applying the known properties of cube, mathematics implies the sufficiency of the upper-level universals to account for human diversity. Implications for rationally based ethical categorical imperatives in education are discussed. [ABSTRACT FROM AUTHOR]

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO's account of function, provide some reasons for favoring it over competing views, and defend it against objections. [ABSTRACT FROM AUTHOR]

SNOMED CT is a large concept -based terminology designed according to epistemic, semantic and pragmatic principles relevant to clinicians. Its goal is structured clinical reporting in electronic healthcare records (EHRs). The Basic Formal Ontology (BFO) is an ontology designed on the basis of types claimed to exist in reality based on a domain-independent ontological theory. Its goal is faithful representation of reality within that theory. The Ontology for General Medical Science (OGMS) extends the BFO by providing definitions for types relevant within the clinical domain. Combining SNOMED CT with the ontological rigor of BFO and OGMS might improve clinical reporting by, f.i., preventing data entry mistakes and inconsistencies, and make EHRs more comparable. To that end, we are developing a logical framework capable of exploiting what SNOMED CT offers terminologically and realism-based ontologies such as the BFO and the OGMS ontologically by means of bridging axioms compatible with the BFO, and expressed in the same CLIF-dialect as used in its axiomatization in first order logic. In this paper, we report on our attempts to detect in the combinations of binary relations that are used in the definition of SNOMED CT's definitions of disorder concepts patterns which might at least partially automate the construction of such axioms. Our findings suggest that this partial automation is indeed possible, but to a smaller extent than we had hoped for. We compare our approach with a recent proposal that seeks to bring SNOMED CT and BFO closer together by reinterpreting SNOMED CT disorders as clinical occurrents. The proposal has its merit in providing a realist underpinning for that part of SNOMED CT's concept model in terms of the BFO, but is not discriminatory enough for an automatic translation into OGMS. Key problem is the lack of face validity of SNOMED CT disorder terms as compared to the formal definitions they are given and this in absence of textual definitions.

Today, Complex African Society; African Traditional Medicine (ATM) is used in parallel to Conventional Medicine (CM). Various attempts have been made to bridge the gap between African Traditional Medicine and Conventional Medicine in order to harmonize treatment and to create equal form of therapeutic cooperation. Although there is some minimal form of collaboration, African Traditional Medicine lacks formal structures; each practitioner has his/her own ways of providing healing services. Knowledge generated from Conventional Medicine is structured unlike African Traditional Medicine whose knowledge is not structured, isolated and mistrusted yet a lot of knowledge is generated in the practices which can be use across whole health sector. In this paper we are proposing ontology as a model to bridge the gap between African Traditional Medicine and Conventional Medicine for the benefit of users. We are proposing a methodology for structuring ATM knowledge as an extension of Basic Formal Ontology (BFO); a standard upper level ontology. [ABSTRACT FROM AUTHOR]

Basic Formal Ontology (BFO), developed by Barry Smith and his colleagues, is a foundational ontology used in information science for the description of entities at the highest level of generality. One of the salient features of BFO is the division of entities into continuants of so-called SNAP (or snapshot) ontology and occurents of so-called SPAN (or spanning time) ontology. The division is motivated by an apparent impasse in the endurantist/perdurantist controversy in recent analytical metaphysics. In this paper, drawing on Aristotle, I suggest a realism-supporting modification of Smith's approach. [ABSTRACT FROM AUTHOR]

Abstract: This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. [Copyright &y& Elsevier]

Abstract: The IPAP Schizophrenia Algorithm was originally designed in the form of a flow-chart to help physicians optimise the treatment of schizophrenic patients in the spirit of guideline-based medicine. We take this algorithm as our starting point in investigating how artifacts of this sort can benefit from the facilities of high-quality ontologies. The IPAP algorithm exists thus far only in a form suitable for use by human beings. We draw on the resources of Basic Formal Ontology (BFO) in order to show how such an algorithm can be enhanced in such a way that it can be used in Semantic Web and related applications. We found that BFO provides a framework that is able to capture in a rigorous way all the types of entities represented in the IPAP Schizophrenia Algorithm in way which yields a computational tool that can be used by software agents to perform monitoring and control of schizophrenic patients. We discuss the issues involved in building an application ontology for this purpose, issues which are important for any Semantic Web application in the life science and healthcare domains. [Copyright &y& Elsevier]

Objective: to identify on the basis of a use case major problem types novices in realism-based ontology design face when attempting to construct an ontology intended to explain differences and commonalities between competing scientific theories., Methodology: an ontology student was tasked (1) to extract manually from a paper about five distinct motivational learning theories the scientific terms used to explain the theories, (2) to map these terms where possible to type-terms from existing realism-based ontologies or create new ones otherwise, (3) to indicate for new type-terms their immediate subsumer, and (4) to document at every step issues that were encountered., Results: where term extraction and type-term assignment were handled satisfactorily, correct classification in function of the BFO was a major challenge. Root causes identified included ambiguous and underspecified term use in the theories, the ontological status of psychological constructs, lack of high quality ontologies for the behavioral sciences and insufficient 'deep' understanding of some BFO entities, in part because of insufficient documentation thereof suitable for learners. The issues the student encountered were often insufficiently described for the instructor to identify the problem without analyzing the source paper itself., Conclusion: whereas behavioral scientists need to do efforts to make their theories comparable, realism-based ontologies can help them therein only when ontology developers and educators put more effort in making them more accessible without violating the principles.

The IPAP Schizophrenia Algorithm was originally designed in the form of a flow-chart to help physicians optimise the treatment of schizophrenic patients in the spirit of guideline-based medicine. We take this algorithm as our starting point in investigating how artifacts of this sort can benefit from the facilities of high-quality ontologies. The IPAP algorithm exists thus far only in a form suitable for use by human beings. We draw on the resources of Basic Formal Ontology (BFO) in order to show how such an algorithm can be enhanced in such a way that it can be used in Semantic Web and related applications. We found that BFO provides a framework that is able to capture in a rigorous way all the types of entities represented in the IPAP Schizophrenia Algorithm in way which yields a computational tool that can be used by software agents to perform monitoring and control of schizophrenic patients. We discuss the issues involved in building an application ontology for this purpose, issues which are important for any Semantic Web application in the life science and healthcare domains.