Process Ontology Research Articles

Processualism and substantialism as two philosophical paradigms

The subject of this research is the advantage of the ontology of process over the ontology of substance in description of the ontological structure of the world. Analysis is conducted on the comparative heuristic potential of essentialism and substantialism on the one hand, and philosophy of the process on the other hand. Essentialism postulates stable, mature, already constituted objects with objectively given essential characteristics that form profound structure of the object. The clearly differentiated array of concepts and categories that reflects the structure of reality and the nature of things is placed on the reality in the flow of becoming. The philosophy of process, in turn, insists on the dynamic and relational nature of reality, and considers time to be the factor constitutive of reality. The fabric of reality is comprised of the processes that relate and interact with other processes forming their dynamic context. The article demonstrates the applicability of the ontology of process in biology, namely on the example of the phenomenon of symbiosis and holobionts. The arguments are provided that the object can be ontologically described as a process; however, a range of processes (for example, photosynthesis) cannot be analyzed in the object categories. Criticism is expressed towards the concept of essential properties of the substance, taking into account perspectivism and variants of the processes of with objects. It is indicated that gradualism characteristics to the philosophy of process allows removing dichotomies and introducing nuances into the binary picture of reality. The novelty of this work consists in highlighting the questions faced by the philosophy of process, namely the question of determination of the status of time essential for determining the process as the basic ontological entity.

PANDA2: protein function prediction using graph neural networks.

High-throughput sequencing technologies have generated massive protein sequences, but the annotations of protein sequences highly rely on the low-throughput and expensive biological experiments. Therefore, accurate and fast computational alternatives are needed to infer functional knowledge from protein sequences. The gene ontology (GO) directed acyclic graph (DAG) contains the hierarchical relationships between GO terms but is hard to be integrated into machine learning algorithms for functional predictions. We developed a deep learning system named PANDA2 to predict protein functions, which used the cutting-edge graph neural network to model the topology of the GO DAG and integrated the features generated by transformer protein language models. Compared with the top 10 methods in CAFA3, PANDA2 ranked first in cellular component ontology (CCO), tied first in biological process ontology (BPO) but had a higher coverage rate, and second in molecular function ontology (MFO). Compared with other recently-developed cutting-edge predictors DeepGOPlus, GOLabeler, and DeepText2GO, and benchmarked on another independent dataset, PANDA2 ranked first in CCO, first in BPO, and second in MFO. PANDA2 can be freely accessed from http://dna.cs.miami.edu/PANDA2/.

An Ontology of Emotion Process to Support Sentiment Analysis

Sentiment analysis is used to mine text data from many sources, including blogs, support forums, and social media, in order to extract customers’ opinions and attitudes. The results can be used to make important assessments about a customer’s attitude toward a company and if and how a company should respond. However, much research on sentiment analysis uses simple classification, where the polarity of a text that is mined is classified as positive, negative, or neutral. This research creates an ontology of emotion process to support sentiment analysis, with an emphasis on obtaining a more fine-grained assessment of sentiment than polarity. The ontology is grounded in a theory of emotion process and consists of concepts that capture the generation of emotion all the way from the occurrence of an event to the resulting behaviors of the person expressing the sentiment. It includes two lexicons: one for affect and one for appraisal. The ontology is applied to posts obtained from customer support forums of large companies to show its applicability in a multilevel evaluation. Doing so provides an example of a complete ontology assessment effort.

Contextual Text Mining Framework for Unstructured Textual Judicial Corpora through Ontologies

Digitalization has changed the way of information processing, and new techniques of legal data processing are evolving. Text mining helps to analyze and search different court cases available in the form of digital text documents to extract case reasoning and related data. This sort of case processing helps professionals and researchers to refer the previous case with more accuracy in reduced time. The rapid development of judicial ontologies seems to deliver interesting problem solving to legal knowledge formalization. Mining context information through ontologies from corpora is a challenging and interesting field. This research paper presents a three tier contextual text mining framework through ontologies for judicial corpora. This framework comprises on the judicial corpus, text mining processing resources and ontologies for mining contextual text from corpora to make text and data mining more reliable and fast. A top-down ontology construction approach has been adopted in this paper. The judicial corpus has been selected with a sufficient dataset to process and evaluate the results. The experimental results and evaluations show significant improvements in comparison with the available techniques.

PHILOSOPHICAL‐CONCEPTUAL APPROACHES TO THE DEFINITION OF GLOBALIZATION

Globalization determines the process of unification of all mankind on the planet Earth. It is the planetary level that outlines the process of "globality". There is a unification of human activity, the development of international trade, increasing capital flows between countries, opening access to foreign resources, including labor markets, there are general trends of integration in the socio-cultural and economic context. This convergence contributes to the strengthening of interaction, integration, and interdependence between nations. In E. Cassirer's philosophy, globalization can be understood as a symbolic form that functions as a worldview in modern discourses. Globalization as a symbolic form has become an image of the world, has changed our understanding of space and time. In the world-system analysis, capitalism is presented as a historical and social system that integrates its achievements into the "world-economy", and it is the methods of modern capitalism that have allowed the modern world economy to go beyond the political borders of individual countries. Against the background of globalization processes in the mass consciousness and public opinion, a contradiction is formed, represented by rational optimism, which gave rise to civilization, and on the other hand, caused a crisis (existential, environmental, economic). The process of globalization has an ontological dimension. This is, above all, a process of expanding the boundaries of reality. From the standpoint of instrumentalism and pragmatism, it is science, education, and democracy that can help to go beyond the temporal and spatial contours of human activity. In the philosophy of technology, attention is paid to the scientific and technological revolution that catalyzed the process of globalization. Globalization creates a complex of the most acute socio-cultural contradictions and requires adequate understanding and research, which can be fruitfully conducted in the framework of philosophical analysis, which in itself has a high level of systemic generalization. The process of globalization has an ontological dimension, which is in the process of expanding the boundaries of reality, both physical and virtual. Within the framework of instrumentalism and pragmatism, globalization is identified with the process of democratization. These ideas are developed in the political philosophy of J. Rawls, who considers it possible to form a model of global justice at the international level. The structuralist approach attempts to formulate an ontology of globalization processes at the level of international relations. In the context of his cosmopolitan views, J. Habermas tries to outline the contours of supranational democracy. Within the social ontology, globalization is seen as a mutually constitutive relationship between analytical-autonomous agents and structures. The position of postmodernists outlines the possibilities of different trajectories of the development of countries in the international arena.

From Action to Cognition: Neural Reuse, Network Theory and the Emergence of Higher Cognitive Functions.

The aim of this article is to discuss the logic and assumptions behind the concept of neural reuse, to explore its biological advantages and to discuss the implications for the cognition of a brain that reuses existing circuits and resources. We first address the requirements that must be fulfilled for neural reuse to be a biologically plausible mechanism. Neural reuse theories generally take a developmental approach and model the brain as a dynamic system composed of highly flexible neural networks. They often argue against domain-specificity and for a distributed, embodied representation of knowledge, which sets them apart from modular theories of mental processes. We provide an example of reuse by proposing how a phylogenetically more modern mental capacity (mental rotation) may appear through the reuse and recombination of existing resources from an older capacity (motor planning). We conclude by putting arguments into context regarding functional modularity, embodied representation, and the current ontology of mental processes.

Associating cognitive reserve and brain‐wide gene expression regarding Alzheimer's disease

AbstractBackgroundCognitive reserve (CR) is susceptibility to brain damages, which impacts the development of Alzheimer’s disease (AD). Whereas CR is associated with certain subnetworks of brain connectivity, little research has been done on identifying genes that contribute to these subnetworks. In this study, we linked these subnetworks to regional variation in brain‐wide gene expression. We utilized Allen Human Brain Atlas (AHBA) in that it comprises gene expression data spanning the whole brain.MethodWe extracted a binary subnetwork regarding CR from AD patients. Then we drew out gene expression patterns in the subnetwork’s regions of interest (ROIs) and constructed a gene network through Weighted Gene Co‐expression Network Analysis (WGCNA). To research the distinctive trait of this sub‐region gene network (SGN), we also constructed a whole‐brain gene network (WGN). We detected modules (clusters of highly interconnected genes) of each network and identified their hub genes (genes with high intra‐modular connectivity). We sought non‐preserved, unique modules in SGN compared to WGN using the median rank statistic. Finally, the biological process ontology of the hub genes was investigated by functional enrichment analysis.ResultWe constructed gene networks based on gene expression data of 10544 genes. WGN consisted of 90 nodes of whole‐brain regions and SGN consisted of 49 nodes of the subnetwork ROIs. While 18 modules were detected in SGN, modules yellow, magenta, red and black were identified as unique modules. Module magenta included novel co‐expressed gene clusters, and the other modules combined genes that were classified as different modules in WGN. Apoptotic process, including apoptosis‐regulation and neuron death, was enriched distinctively in the 4 non‐preserved modules. Neuronal death due to apoptosis is a common pathological feature in the brains of AD patients.ConclusionWe identified brain‐wide gene co‐expression modules that have unique specific connectivity patterns related to the CR subnetwork. This non‐preservation highlights the relevance of CR and gene expression patterns. Moreover, the modules were enriched for AD risk genes, further demonstrating the functional context of CR in AD. This study will provide the groundwork for novel insights and extensive research to associate brain‐wide gene expression and connectome‐wide phenotype regarding AD.

Development of ontology-based model to support learning process in LMS

<p>E-Learning is an important support mechanism for educational systems to increase the efficiency of the education process including students and teachers. The current e-learning systems typically lack the level of metacognitive awareness, adaptive tutoring, and time management skills and have not always met the expectations of the learners as required. In this study, we introduce a novel ontological model for the learning process in the e-learning domain. In the framework, we have built a domain ontology that represents knowledge of the learning, the outcome domain ontology covers the whole learning process. We focused on the learning process ontology model conceptualizing knowledge constructions, such as learning courses, and we present the created course and learning process ontology in detail. In this work, we considered three layers of learning process. The top layer defines a general framework of learning process, conceptual model layer, defines the framework of the actual process of the learning process and course ontology model contains the knowledge unit of the learning process. The prototype ontology is constructed in protégé and managed by Java web ontology language-application programming interface (OWL-API). As a result, our model can solve the problems of current e-tutor systems. Also, it can be used for different domain in e-tutor systems. It can reach the characteristics of standardization, reusability, flexibility, and open knowledge. By applying this model, we can avoid applying isolated databases. The constructed ontology can be used in the future to control adaptive intelligent e-tutor frameworks.</p>

The Performative Power of Frictions and New Possibilities: Studying power, performativity and process with Follett’s pragmatism

This article seeks to open up new possibilities for process organization studies to reimagine power and performativity by exploring the potential of Mary Parker Follett’s pragmatism as process philosophy. I revisit her body of work to show how she translated her process ontology into theoretical resources and practical insights that allow for new ways of understanding power and performativity together and explore them as mutually constituting processes of organizing. In particular, I mobilize Follett’s view of conflicts as emerging differences in the world and frictions as constructive conflicts with the potential to generate something new in order to introduce and conceptualize ‘performative power’, that is, the power emerging from relating and integrating differences in organizational situations that are experienced as frictions by people involved. Drawing on my ethnographic study of an entrepreneurship accelerator – a training programme for innovators and start-up projects – I discuss and illustrate empirically how performative power is generated from frictions that arise in ordinary lived experiences. This conceptualization of performative power is an attempt to develop a processual and performative understanding of power, and a useful lens to conduct process research. Making a connection between performative power and the experience of frictions provides a new way to see, talk and study power processually in contemporary organizations.

Re-imagining the dialogic spaces of talanoa through Samoan onto-epistemology

This article proposes a Samoan indigenous philosophical position to reconceptualise the dialogic spaces of talanoa; particularly how talanoa is applied methodologically to research practice. Talanoa within New Zealand Pacific research scholarship is problematised, raising particular tensions of the universal and humanistic ideologies that are entrenched within institutional ethics and research protocols. The dialogic relational space which is embedded throughout talanoa methodology is called into question, evoking alternative ways of knowing and being within the talanoa research assemblage[1] (including the material-world). Samoan epistemology reveals that nature is constituted within personhood (Vaai & Nabobo-Baba, 2017) and that nature is co-agentic with human in an ecology of knowing. We call for a shift in thinking material-ethics that opens talanoa to a materialist process ontology, where knowledge generation emerges through human and non-human encounters.
 
 
 [1] The concept of assemblage developed by Deleuze and Guattari (1987) refers to a process of temporary arrangements or constellations of objects, expressions, bodies, qualities and territories that create new ways of functioning. The assemblage is a multiplicity shaped by a wide range of flows and emerges from the arranging process of heterogenous elements (Livesey, 2010).

Biobehavioral organization shapes the immune epigenome in infant rhesus Macaques (Macaca mulatta)

How individuals respond to and cope with stress is linked with their health and well-being. It is presumed that early stress responsiveness helps shape the health of the developing organism, but the relationship between stress responsiveness and early immune function during development is not well-known. We hypothesized that stress responsiveness may shape epigenetic regulation of immune genes in infancy. We investigated whether aspects of behavioral responsiveness and hypothalamic-pituitary adrenal stress-response were associated with epigenome-wide immune cell DNA methylation patterns in 154 infant rhesus monkeys (3–4 months old). Infants’ behavioral and physiological responses were collected during a standardized biobehavioral assessment, which included temporary relocation and separation from their mother and social group. Genome-wide DNA methylation was quantified using restricted representation bisulfite sequencing (RRBS) from blood DNA collected 2-hours post-separation. Epigenome-wide analyses were conducted using simple regression, multiple regression controlling for immune cell counts, and permutation regression, all corrected for false discovery rate. Across the variables analyzed, there were 20,368 unique sites (in 9,040 genes) at which methylation was significantly associated with at least one behavioral responsiveness or cortisol measure across the three analyses. There were significant associations in 442 genes in the Immune System Process ontology category, and 94 genes in the Inflammation mediated by chemokine and cytokine signaling gene pathway. Out of 35 candidate genes that were selected for further investigation, there were 13 genes with at least one site at which methylation was significantly associated with behavioral responsiveness or cortisol, including two intron sites in the glucocorticoid receptor gene, at which methylation was negatively correlated with emotional behavior the day following the social separation (Day 2 Emotionality; β = −0.39, q < 0.001) and cortisol response following a relocation stressor (Sample 1; β = −0.33, q < 0.001). We conclude that biobehavioral stress responsiveness may correlate with the developing epigenome, and that DNA methylation of immune cells may be a mechanism by which patterns of stress response affect health and immune functioning.

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.

With the explosive growth of protein sequences, large-scale automated protein function prediction (AFP) is becoming challenging. A protein is usually associated with dozens of gene ontology (GO) terms. Therefore, AFP is regarded as a problem of large-scale multi-label classification. Under the learning to rank (LTR) framework, our previous NetGO tool integrated massive networks and multi-type information about protein sequences to achieve good performance by dealing with all possible GO terms (>44 000). In this work, we propose the updated version as NetGO 2.0, which further improves the performance of large-scale AFP. NetGO 2.0 also incorporates literature information by logistic regression and deep sequence information by recurrent neural network (RNN) into the framework. We generate datasets following the critical assessment of functional annotation (CAFA) protocol. Experiment results show that NetGO 2.0 outperformed NetGO significantly in biological process ontology (BPO) and cellular component ontology (CCO). In particular, NetGO 2.0 achieved a 12.6% improvement over NetGO in terms of area under precision-recall curve (AUPR) in BPO and around 2.6% in terms of n}{}mathbf {F_{max}} in CCO. These results demonstrate the benefits of incorporating text and deep sequence information for the functional annotation of BPO and CCO. The NetGO 2.0 web server is freely available at http://issubmission.sjtu.edu.cn/ng2/.

How managers frame and make sense of unexpected events in project implementation

This paper examines how managers’ framing and sensemaking of unexpected events alters and adapts over time during the course of a major project implementation. By adopting a process ontology, we study the temporal evolution of framing and sensemaking of unexpected events and how they recursively influence each other. We show how over time managers’ sensemaking shifts from one form of sensemaking to another as they frame and reframe events to cope with changes in their environment.Our study contributes in two important ways. First, we contribute to the discussions on framing and sensemaking literature by illustrating how they manifest recursively. In particular, we show how change in framing of events alters the form of sensemaking and how new forms of sensemaking enable actors to reframe their expectations. Second, we contribute to discussions on how project managers cope with unexpected events in large complex projects which may lead to failures or project termination. We show how unexpected events not only disrupt actors’ mental frames of what and how to accomplish as part of project implementation, but also how they rework their expectations to adapt and move forward.

Competing Ontologies: A Redux Primer for Public Administration

Over the last decade, a growing number of public administration theorists have taken up the question of how ontology—assumptions about the nature of existence—shapes our understanding of governance. This substantially updated primer, originally published in Public Administration Review, introduces the essay, provides a basic explanation of ontology, describes the fundamental debates in philosophies of ontology, and discusses why ontology is important to social and political theory and therefore public administration theory and practice. Using an ideal-type approach grounded in differing ontological assumptions, a Governance Typology is provided to support analysis of differing public administration theories. An integrative approach to governance is offered that is grounded in relational process ontology—a foundation that may support a viable synthesis of the other four primary ideal-types. The essay concludes with a call for personal reflection on the part of scholars and practitioners regarding their own ontological commitments and an invitation to collaborative inquiry.

Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7

Myogenic regulatory factors (MRFs) such as MyoD , Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly ( P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly ( P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP. How to cite: Sodhi SS, Sharma N, Ghosh M, et al. Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.03.001

Powers, Processes, and Time

In this paper I argue that even the most radical metaphysics of powers (such as that adopted by Mumford and Anjum, Cartwright, or Groff) are compatible with eternalism. I first offer a taxonomy of powers ontologies, and attempt to characterise the difference between moderate and radical powers ontologies—the latter are characterised by an emphasis on production and dynamicity. I consider an argument by C. Friebe to the effect that the productive character of powers is inconsistent with Eternalism and find it wanting. I then elucidate the notion of dynamicity that radical powers theorists employ by making apparent their link with an ontology of irreducible processes. Finally, I respond to an argument by Donatella Donati to the effect that eternalism entails a reductive account of change which is inconsistent with process ontologies, and show that the the two are compatible. I conclude that we have no reason to think that radical powers metaphysics (and, a fortiori, every powers ontology) are not compatible with eternalism.

Aligning BIM and ontology for information retrieve and reasoning in value for money assessment

Value for money (VfM) assessments often lack effective automatic processes and reasoning support in public-private partnership (PPP) projects. To automate these assessments, this paper proposes a comprehensive approach that aligns with the goals of building information modeling (BIM) as the necessary information support and ontology for the knowledge process. The main contribution of this work is the retrieval of information from the BIM environment with the ontological knowledge base to enable more efficient and persuasive methods for project and finance management that facilitate decision-making rather than an experience-based approach. The constructed ontology can also be reused and further expanded to include project needs from end-user perspectives. This work is expected to further the research on expanding semantic BIM-based decision making in different infrastructure procurement projects.

PROCESS-BASED ENTITIES ARE RELATIONAL STRUCTURES. From Whitehead to Structuralism

Abstract The aim of this work is to argue for the idea that processes and process-based entities are to be modelled as relational structures. Relational structures are genuine structures, namely entities not committed to the existence of basic objects. My argument moves from the analysis of Whitehead’s original insight about process-based entities that, despite some residual of substance metaphysics, has the merit of grounding the intrinsic dynamism of reality on the holistic and relational characters of process-based entities. The current model of process ontology requires genuine emergence and this, in turn, requires organizations, i.e., emergence in organizations. Another view about processes rely on a structural specification of processes. I suggest that the two views can be made compatible by the help of a specific sort of structures, namely relational structures. The appeal to the mathematical theory of genuine structures, category theory, reveals the formal plausibility of this convergence. According to this formal approach, genuine structures are essentially dynamic entities for they are relational, namely, as well as organizations, they are not existentially committed to particulars.

Use of a modular ontology and a semantic annotation tool to describe the care pathway of patients with amyotrophic lateral sclerosis in a coordination network.

The objective of this study was to describe the care pathway of patients with amyotrophic lateral sclerosis (ALS) based on real-life textual data from a regional coordination network, the Ile-de-France ALS network. This coordination network provides care for 92% of patients diagnosed with ALS living in Ile-de-France. We developed a modular ontology (OntoPaRON) for the automatic processing of these unstructured textual data. OntoPaRON has different modules: the core, medical, socio-environmental, coordination, and consolidation modules. Our approach was unique in its creation of fully defined concepts at different levels of the modular ontology to address specific topics relating to healthcare trajectories. We also created a semantic annotation tool specific to the French language and the specificities of our corpus, the Ontology-Based Semantic Annotation Module (OnBaSAM), using the OntoPaRON ontology as a reference. We used these tools to annotate the records of 928 patients automatically. The semantic (qualitative) annotations of the concepts were transformed into quantitative data. By using these pipelines we were able to transform unstructured textual data into structured quantitative data. Based on data processing, semantic annotations, sociodemographic data for the patient and clinical variables, we found that the need and demand for human and technical assistance depend on the initial form of the disease, the motor state, and the patient age. The presence of exhaustion in care management, is related to the patient's motor and cognitive state.

Онтологическая система «знания-деятельность»

The paper considers an approach to construction of human rational activity ontological description. Such a description can serve as an additional source for entering the information space, expands the class of possible indexes for describing documents and allows to implement contextual search. The purpose and features of the use of ontologies in describing the subject area, both from a theoretical and an applied point of view, are considered. Criteria for identifying types of ontologies are indicated. Based on the principles of knowledge schematism, a knowledge representation ontologies system has been developed, which unites language, forms of knowledge representation and process schemes. It is shown that precisely such kind of ontologies system makes possible the practical use of ontologies in computing environments. For a comprehensive description of production (rational) activity, ontologies of artifacts and processes are presented, developed on the basis of an analysis of state and international standards. The ontology of an artifact is a description of an object - a means and a result of purposeful activity, an ontology of processes is a formalized description of the life cycle of an activity. With the help of the ontology of the artifact, it becomes possible to represent the logical structure of activity, and with the help of the ontology of processes, the temporal structure, which jointly determine the two sides of the description of complex activity. The proposed ontology of processes includes a hierarchically related set of stages of the life cycle of activity, objects and subjects of activity of each stage and plays the role of a "navigation map" for subjects of activity, allowing them to navigate in complex organizational structures.