Process Ontology Research Articles

Developing a Logistics Ontology for Natural Language Processing

The business area requires the presence of Supply Chain services, to respond to the constantly evolving requirements. Supply chains are dynamic networks that include a continuous flow of processes, starting with the supplier and ending with the customer. For effective supply chain management, a conceptual understanding of the knowledge underlying this field is of utmost importance. On the other hand, ontologies are considered one of the most appropriate ways of representing knowledge and valuable tools for decision-making situations. The purpose of this paper is to present an ontology created to identify the common concepts of supply chain management systems, with the ultimate goal of supporting and promoting Natural Language Processing technologies through the representation of terminological knowledge for this specific field.

The ontology of coevolution beyond economic systems

AbstractThis paper provides an analysis of the general ontology of coevolutionary processes. I argue that to properly understand the ontological phenomenon of coevolution, we need to move away from neophobic, flat, and substance-based ontologies and adopt a pluralist and emergentist process metaphysics that takes into account both horizontal and vertical codetermination. Following this approach, I differentiate between ontological (co)evolution in a general and specific sense. General (co)evolution can be observed in physical and chemical matter. Before the emergence of living matter, the universe evolved, achieving more ontological complexity and qualitative density. Since physical and chemical matter are made up of a complex interplay of continuities and discontinuities, physical and chemical entities and processes are multiple and codetermine each other through a dynamic complex patterning, as basically described by what the Spanish philosopher Gustavo Bueno called symploké following Plato’s Sophist. Therefore, physical and chemical evolutionary processes are more accurately described as coevolutionary processes. On the other hand, specific coevolution can be observed in the biological, social, and cultural/artificial realms. Its ontological specificity lies in the dynamic interactions of novelty, replication, and selection, which are absent in physical and chemical matter. In conclusion, I argue that rather than unnecessarily complicating our view of reality, this approach is manageable epistemologically and allows for a better understanding of dynamic codetermination in the universe, from physical matter to cultural spheres.

Breaking bad? Playing the fool and constructing the ‘bad researcher’ in entrepreneurship

How to deal with grand challenges and the crisis of knowledge production and their implications for entrepreneurial research and practice is a topic of growing interest. In this paper we argue that we need to rethink who is involved in entrepreneurship research and how that research is conducted and communicated. This begins by moving beyond the traditional ostensible objective separation of the ‘researcher’ from the ‘research subject’ to adopt a posthuman and post-qualitative inquiry perspective that questions the dominant position of the human subject and challenges the humanistic belief in the essential, conscious and intentional human as the primary source of agency. As such, it adopts a process ontology, stresses hybridity and difference and encourages experimentation. This requires us to become ‘bad researchers’, undertaking subversive research that goes beyond the oppositions of quantitative/qualitative and foundationalist/non-foundationalist. In this we take the ‘fool’ (jester, trickster) as our guide. Historically associated with inversion, usurping authority and putting down the mighty the fool is a liminal character who has the duty to ask all those questions that no one else dares to ask. The paper concludes with suggestions as to how this may inform a re-newed entrepreneurship for the crisis-laden twenty first century.

An Ontology of Properties and Processes of Inorganic Materials Based on Context-Dependency and Its Use

An Ontology of Properties and Processes of Inorganic Materials Based on Context-Dependency and Its Use

Identifying Terms to Represent Concepts of a Work Process Ontology

Objectives: To identify ontology concepts from text documents for the construction of work process ontology. Methods: This study proposes a methodology to identify terms representing a work process ontology concept from a document. The methodology encompasses several key steps: document collecting, text pre-processing, term weighting and analysis, terms mapping, and domain expert relevance judgments. A comparison between the results of three different term weighting schemes, namely the Term Frequency (TF), Term Frequency-Inverse Document Frequency (TFIDF), and Mutual Information (MI) is made with the ontology concept that the domain expert has judged. Findings: The approaches adopted in this study have managed to extract ontological concepts from the targeted domain knowledge source. The findings of the comparison analysis suggest that the TFIDF term weighting scheme exhibits better results compared to the TF and MI weighting schemes. Novelty: A work process ontology is a structured knowledge describing daily operations in the government sector. However, there has been little to no effort in building the work process ontology. This study presents an integrated approach for identifying ontology concepts from documents within the domain of the work process. To the utmost extent of our understanding, this research initiative is the initial attempt to introduce a structured methodology for the semi-automatic extraction and evaluation of concepts and relationships within this domain. The findings can be utilised as a foundation for developing an ontology in the specific field. Keywords: Ontology, Work process, Text extraction, Natural language processing, Term weighting

Conceptual analysis of sensitive business processes

PurposeThis paper introduces the problematic of the SBP modeling. Our objective is to provide a conceptual analysis related to the concept of SBP. This facilitates, on the one hand, easier understanding by business analysts and end-users, and one the other hand, the integration of the new specific concepts relating to the SBP/BPM-KM domains into the BPMN meta-model (OMG, 2013).Design/methodology/approachWe propose a rigorous characterization of SBP (Sensitive Business Processes) (which distinguishes it from classic, structured and conventional BPs). Secondly, we propose a multidimensional classification of SBP modeling aspects and requirements to develop expressive, comprehensive and rigorous models. Besides, we present an in-depth study of the different modeling approaches and languages, in order to analyze their expressiveness and their abil-ity to perfectly and explicitly represent the new specific requirements of SBP modeling. In this study, we choose the better one positioned nowadays, BPMN 2.0, as the best suited standard for SBP representation. Finally, we propose a semantically rich conceptualization of a SBP organized in core ontology.FindingsWe defined a rigorous conceptual specification for this type of BP, organized in a multi-perspective formal ontology, the Core Ontology of Sensitive Business Processes (COSBP). This reference ontology will be used to define a generic BP meta-model (BPM4KI) further specifying SBPs. The objective is to obtain an enriched consensus modeling covering all generic concepts, semantic relationships and properties needed for the exploitation of SBPs, known as core modeling.Originality/valueThis paper introduces the problem of conceptual analysis of SBPs for (crucial) knowledge identification and management. These processes are highly complex and knowledge-intensive. The originality of this contribution lies in the multi-dimensional approach we have adopted for SBP modeling as well as the definition of a Core Ontology of Sensitive Business Processes (COSBP) which is very useful to extend the BPMN notation for knowledge management.

Business View Specification of Enterprise Information Systems Based on Core Ontologies

Enterprise Information Systems (EIS) supporting Business Processes (BPs), particularly Sensitive Business Processes (SBPs), should be characterized by integrity, flexibility, and interoperability. However, the urbanization approach, which we rely on to implement these systems, must address the “three fit” problems that hinder the realization of these desired features at both the business and technical infrastructures: “vertical fit” problems – concerning the business infrastructure; “horizontal fit” problems and “transversal fit” problems – concerning the technical infrastructure. We argue that for overcoming those problems, it is necessary to define an explicit framework for specifying BPs/SBPs. We present in this paper our conceptual specification for the BPs/SBPs modeling domain in the form of a core domain ontology, in order to overcome “horizontal fit” and “transversal fit” problems. Specifically, we introduce (i) our reference ontological framework and (ii) provide an overview of the Core Ontology of Sensitive Business Processes (COSBP). Our focus lies in the representation of SBPs in order to overcome “vertical fit” problems.

On the relationship between scientific theory and ontology in everything flows.

In their anthology Everything Flows: Towards a Processual Philosophy of Biology, Daniel J. Nicholson and John Dupré argue that modern theories of biology imply that the fundamental structure of reality is processual at its core. In the present work, I first examine the implicit and explicit metaphysical presuppositions the editors make in order to allow for such an inference from scientific theory to ontology. After showing the difficulties of a naïve transfer of theoretical entities to fundamental ontology, I argue that the editors can nevertheless extend their claims beyond the mere articulation of different domain ontologies. This leads to the idea of a scientifically informed induction base for an ontology of processes.

Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.

One significant challenge in addressing the coronavirus disease 2019 (COVID-19) pandemic is to grasp a comprehensive picture of its infectious mechanisms. We urgently need a consistent framework to capture the intricacies of its complicated viral infectious processes and diverse symptoms. We systematized COVID-19 infectious processes through an ontological approach and provided a unified description framework of causal relationships from the early infectious stage to severe clinical manifestations based on the homeostasis imbalance process ontology (HoIP). HoIP covers a broad range of processes in the body, ranging from normal to abnormal. Moreover, our imbalance model enabled us to distinguish viral functional demands from immune defense processes, thereby supporting the development of new drugs, and our research demonstrates how ontological reasoning contributes to the identification of patients at severe risk. The HoIP organises knowledge of COVID-19 infectious processes and related entities, such as molecules, drugs, and symptoms, with a consistent descriptive framework. HoIP is expected to harmonise the description of various heterogeneous processes and improve the interoperability of COVID-19 knowledge through the COVID-19 ontology harmonisation working group.

Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective

Although cellular senescence is a key factor in organismal aging, with both positive and negative effects on individuals, its mechanisms remain largely unknown. Thus, integrating knowledge is essential to explain how cellular senescence manifests in tissue damage and age-related diseases. Here, we propose an ontological model that organizes knowledge of cellular senescence in a computer-readable form. We manually annotated and defined cellular senescence processes, molecules, anatomical structures, phenotypes, and other entities based on the Homeostasis Imbalance Process ontology (HOIP). We described the mechanisms as causal relationships of processes and modelled a homeostatic imbalance between stress and stress response in cellular senescence for a unified framework. HOIP was assessed formally, and the relationships between cellular senescence and diseases were inferred for higher-order knowledge processing. We visualized cellular senescence processes to support knowledge utilization. Our study provides a knowledge base to help elucidate mechanisms linking cellular and organismal aging.

A study on formalizing the knowledge of data curation activities across different fields.

In recent years, with the trend of open science, there have been many efforts to share research data on the internet. To promote research data sharing, data curation is essential to make the data interpretable and reusable. In research fields such as life sciences, earth sciences, and social sciences, tasks and procedures have been already developed to implement efficient data curation to meet the needs and customs of individual research fields. However, not only data sharing within research fields but also interdisciplinary data sharing is required to promote open science. For this purpose, knowledge of data curation across the research fields is surveyed, analyzed, and organized as an ontology in this paper. As the survey, existing vocabularies and procedures are collected and compared as well as interviews with the data curators in research institutes in different fields are conducted to clarify commonalities and differences in data curation across the research fields. It turned out that the granularity of tasks and procedures that constitute the building blocks of data curation is not formalized. Without a method to overcome this gap, it will be challenging to promote interdisciplinary reuse of research data. Based on the analysis above, the ontology for the data curation process is proposed to describe data curation processes in different fields universally. It is described by OWL and shown as valid and consistent from the logical viewpoint. The ontology successfully represents data curation activities as the processes in the different fields acquired by the interviews. It is also helpful to identify the functions of the systems to support the data curation process. This study contributes to building a knowledge framework for an interdisciplinary understanding of data curation activities in different fields.

Событийная онтологическая модель экономических отношений

The paper examines the issue of the development of ontologies in the economic domain. The essential role of ontologies in the digitalization of the economy is determined. The author considers the origin of ontologies in philosophy and the transition of ontologies from philosophy to computer science. The paper shows the growth of semantic content and the range of applications of ontologies as they develop. Ontologies in computer science have grown from the tasks of forming a thesaurus to the issues of forming semantic models of subject areas, which makes them close, in terms of generality and depth of approach, to philosophical ontologies. Currently, there are a sufficient number of successful examples of the use of information ontologies, nevertheless, these achievements are disproportionately less than the potential inherent in ontologies. In addition, there is a decrease in interest in ontologies and the number of studies. To determine the reasons for this, the concepts underlying the formation of ontologies are considered. The most promising set of concepts for the formation of ontology in the economic subject field is proposed. It is determined that one of the reasons for the insufficient development of ontologies is the insufficient elaboration of the concepts of ‘economic cell’ and ‘event’ as the basis for reflecting economic processes. The concept of ‘events’ is formulated, which corresponds to the dynamic approach in the formation of ontologies. It is proposed to consider an event in the subject area of economic relations as a change in the values of observed attributes (OMECVA). According to the OMECVA concept, events are primary in cognition and in reflecting the subject area. The informational reflection of objects is considered as a cluster of signs and their meanings in structure, space and time. Three types of events are distinguished: events in the subject area, events of cognition of changes in the subject area and events that change the model of cognition. As a starting point for the development of a promising ontology of economic processes, it is proposed to use accounting as a widespread information system that forms the bulk of economic information. It is proposed to consider a triplet as an economic cell: an economic entity, a type of economic and legal relations, an economic object. Each of these elements is an economic category and a feature in the context of which economic events are characterized.

How Should We Slice Up the Executive Function Pie? Striving Toward an Ontology of Cognitive Control Processes

AbstractThere is a vast literature on executive functioning, or the control of one's thoughts and actions in pursuit of a goal. This broad construct is conceptualized as comprising multiple executive functions (EFs) that support academic achievement and other important life outcomes. However, there is a lack of consensus regarding what, exactly, these core EFs are. This commentary briefly reviews a few dominant models of EFs in developmental and cognitive psychology and outlines issues to be addressed; it then illustrates how insights from neuroscience could help us eliminate redundant terminology and identify EFs that have been largely overlooked. Reaching a consensus regarding the core set of EFs will inform efforts to scaffold EF development and improve educational outcomes.

Development and application of Chinese medical ontology for diabetes mellitus

ObjectiveTo develop a Chinese Diabetes Mellitus Ontology (CDMO) and explore methods for constructing high-quality Chinese biomedical ontologies.Materials and methodsWe used various data sources, including Chinese clinical practice guidelines, expert consensus, literature, and hospital information system database schema, to build the CDMO. We combined top-down and bottom-up strategies and integrated text mining and cross-lingual ontology mapping. The ontology was validated by clinical experts and ontology development tools, and its application was validated through clinical decision support and Chinese natural language medical question answering.ResultsThe current CDMO consists of 3,752 classes, 182 fine-grained object properties with hierarchical relationships, 108 annotation properties, and over 12,000 mappings to other well-known medical ontologies in English. Based on the CDMO and clinical practice guidelines, we developed 200 rules for diabetes diagnosis, treatment, diet, and medication recommendations using the Semantic Web Rule Language. By injecting ontology knowledge, CDMO enhances the performance of the T5 model on a real-world Chinese medical question answering dataset related to diabetes.ConclusionCDMO has fine-grained semantic relationships and extensive annotation information, providing a foundation for medical artificial intelligence applications in Chinese contexts, including the construction of medical knowledge graphs, clinical decision support systems, and automated medical question answering. Furthermore, the development process incorporated natural language processing and cross-lingual ontology mapping to improve the quality of the ontology and improved development efficiency. This workflow offers a methodological reference for the efficient development of other high-quality Chinese as well as non-English medical ontologies.

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific functional category containing multiple child ontologies, and the relationships of parent and child ontologies create a directed acyclic graph. Protein functions are categorized using GO, which divides them into three main groups: cellular component ontology, molecular function ontology, and biological process ontology. Therefore, the GO annotation of protein is a hierarchical multilabel classification problem. This hierarchical relationship introduces complexities such as mixed ontology problem, leading to performance bottlenecks in existing computational methods due to label dependency and data sparsity. To overcome bottleneck issues brought by mixed ontology problem, we propose ProFun-SOM, an innovative multilabel classifier that utilizes multiple sequence alignments (MSAs) to accurately annotate gene ontologies. ProFun-SOM enhances the initial MSAs through a reconstruction process and integrates them into a deep learning architecture. It then predicts annotations within the cellular component, molecular function, biological process, and mixed ontologies. Our evaluation results on three datasets (CAFA3, SwissProt, and NetGO2) demonstrate that ProFun-SOM surpasses state-of-the-art methods. This study confirmed that utilizing MSAs of proteins can effectively overcome the two main bottlenecks issues, label dependency and data sparsity, thereby alleviating the root problem, mixed ontology. A freely accessible web server is available at http://bliulab.net/ ProFun-SOM/.

Speciation and species: a process perspective

Abstract This perspective article proposes that we should think of speciation in the context of a general processual ontology, in which organisms and lineages are seen as central, interdependent processes. It explains what is implied by process ontology with the example of the organism, to illustrate that processes can be persistent individuals, though generally requiring active stabilization. It then explores the idea that speciation should be seen as a bifurcation of a lineage. The relevant notion of species, as a temporal part of an evolving lineage, is narrower than the most inclusive basal taxonomic unit, so speciation in this sense is not applicable to all organisms. The lineage as concrete process is an evolved entity, and hence organisms pre-existed lineages and may still exist outside them.

Scientific fundamentals of building an innovative intelligent system of managing the production of entomophages

The article is devoted to the issue of improving information and technical support for the production of entomophages, in particular, the scientific foundations of building an innovative intelligent system for managing the production of entomophages. The purpose of the research is to develop the scientific basis for building an innovative intelligent system for controlling the production of entomophages. The object of research is the process of managing the production of entomophages. Research methods – structural synthesis, ontological-synergistic and neural network approaches, analysis of T. Saati hierarchies, Bayes network, cognitive and correlational analysis, computer modeling. An innovative intelligent control system for the production of the entomophagеs Habrobracon hebetor was developed based on the results of own research, the technological experience of specialists and modern methods of intellectual data analysis. The structure of the control system is presented. Management processes, software tools and management system innovations are displayed in the form of an associative map. An ontology of processes for innovative intelligent production management of the entomophage Habrobracon hebetor has been developed. The knowledge base of the innovative intelligent control system is presented in the form of facts and production rules. The results of the research increase the level of intellectualization of the processes of managing the production of entomophages, reduce the uncertainties in the management processes, increase the level of informatization and competence of the operator-technologist and are the basis for the development of a theory of decision-making in the production of biological means of plant protection.

Нарциссическая культура и проблема политической легитимации

The work continues the rethinking by the authors of the phenomena of changes in education, science and the structure of power in the 21st century within the framework of the philosophy of culture. The concepts of “carnival” according to M.M. Bakhtin, “the soul of culture” according to O. Spengler, Dionysianism (and neo-paganism) by F. Nietzsche are used for this work. The central problem of this study is the legitimation of the political regime of liberal democracy in the context of a narcissistic culture. The latter, due to its internal characteristics, does not allow the existence of any internal authority, the approval of which would provide a moral sanction to the rule of certain political actors. History provides several options for the ontology of the legitimation process. The fi rst of them are associated with the priesthood that existed in the conditions of the domination of pagan culture, the Abrahamic religions that replaced it developed their own sacred mechanisms for granting sanctions to power. The most important shift occurs during the Modern: mass culture is forming, the role of moral authority is shifting from priests to scientists. To achieve legitimacy, political actors must ensure the progress of society on the basis of new advances in science and technology. The legitimacy is also challenged with the help of scientifi c argumentation – the authorities are presented with claims of erroneous technical and economic decisions that have entailed negative socioeconomic and/or environmental consequences. An extreme but signifi cant case is the challenge of scientifi c foundations of politics, as was the case in the case of Soviet Marxism. Expanded reproduction of science and education in the 20th century erodes the former exclusivity of the scientifi c elite and at the same time eliminates the scientist mechanism of political legitimation. The situation is reversed: now, in order to continue pursuing science and education, the former authorities must prove their usefulness to the authorities and society. But the same thing happens with the authorities themselves: offi cials and deputies turn into “servants of people” and explain their necessity to society with the help of representatives of the humanities. They do not rule anymore but produce public goods in exchange for taxes. Bakhtin’s carnival is triumphing. The regime of liberal democracy that ensured the protection of rights of minorities is close to narcissistic culture, in the center of which is the need for freedom and self-realization of the individual. At the same time, however, any authority – political or scientifi c – has a conditional legitimacy here. The proportion of partisans is growing – actors who recognize the legality of the existing social order but deny its internal justice. Fragility and instability are inherent in liberal democracy. The longevity of such a political regime is ensured by the rise of neo-paganism. Unlike previous pagan cults there is no separate social group of sacrifi ces. Thus, the problem of legitimation is removed: what is already there automatically becomes legitimate. With the help of the liberal discourse, each individual political personality is instilled that it has all the full rights, and the state is left with only responsibilities for the service of this personality: this is the uncontested meaning of Fukuyama’s ‘last man’.

Technics and Contingency

This text aims to explore the relationship between technics and contingency within a context where computational technologies often have the effect of domesticating the latter, leading to its statistical reduction within the realm of the probable. I will argue that the post-prosthetic and non-correlational character of these technologies prompts us to pursue a line of inquiry that calls for a different understanding of contingency. Instead of solely assigning it to domains external to computational technologies (the ‘externality thesis’), this perspective identifies a form of contingency inherent in these technologies themselves (the ‘internality thesis’). I will develop this approach through a comparative analysis of the work of M. Beatrice Fazi and Mark B.N. Hansen, authors who both draw from Alfred N. Whitehead’s process ontology. I will underscore the tensions between their proposals, trying to identify the main divergences within their speculative ontologies of computation. However, I will also propose that we can read them as complementary propositions that account for the ontological productivity of computational media and operations, allowing us to theorise a form of computational contingency independent from the tendencies towards algorithmic closure and determinism present in contemporary technical systems.

Genome-Wide Identification of Selenium-Responsive MicroRNAs in Tea Plant (Camellia sinensis L. O. Kuntze)

Anadequate selenium (Se) intake can enhance human immunity and prevent diseases development. About one billion people in the world have varying degrees of Se deficiency in the world. Organic Se from tea infusion is the most easily absorbed and utilized Se form by the human body. Therefore the production of tea plants rich in Se is an effective way to increase Se dietary intake, but there are few studies on the involvement and functions of miRNAs in the responses of tea plants after Se treatment. MicroRNAs (miRNAs) are endogenous (non-coding) single-stranded RNAs that play crucial roles in regulating plant nutrient element acquisition and accumulation. Physiological analysis discovered that the total Se content in tea plant roots markedly increased under 0.05 mmol·L−1 selenite treatment, with no toxicity symptoms in the leaves and roots. To screen the miRNAs responsive to Se treatment in tea plants, miRNA libraries were constructed from the tea cultivar “Echa 1”. Using high-throughput sequencing, 455 known miRNAs and 203 novel miRNAs were identified in this study. In total, 13 miRNAs were selected that were differentially expressed in tea plants’ roots under 0.05 mmol·L−1 selenite treatments. Gene Ontology enrichment analysis revealed that the target genes of the differentially expressed miRNAs mainly belonged to the metabolic process, membrane, and catalytic activity ontologies. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested that beta-alanine, taurine, hypotaurine, and sulfur metabolism were the most enriched pathways among the differentially expressed miRNAs, implying their involvement in Se accumulation and tolerance in tea plants. Further characterization of the data revealed that the number of novel miRNAs was comparable to that of known miRNAs, indicating that novel miRNAs significantly contributed to the regulation of Se accumulation in tea plant roots. Thisstudy lays the foundation for further research on the regulatory mechanisms underlying Se accumulation and tolerance in tea plants, providing targets to molecular breeding strategies for improving tea nutritional properties.