Process Ontology Research Articles

From internationalization to evolution: The Uppsala model at 40 years

Abstract The original Uppsala model that was published in 1977 explains the internationalization process of firms. We have further developed the model several times in the intervening years. The present article is our latest effort: a general model of the evolution of the multinational business enterprise (MBE), from early steps abroad to being a global firm. The updated, augmented model explains MBE evolution in general, not only characteristics of the internationalization process in a narrow sense. We believe that the newest iteration, anchored in process ontology, will be useful in conducting longitudinal empirical studies.

The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes

BackgroundHigh-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods such as bio-ontologies to extract and share valuable information. In parallel, the development of recent whole-cell models using a systemic cell description opened alternatives for data integration. Integrating a systemic cell description within a bio-ontology would help to progress in whole-cell data integration and modeling synergistically.ResultsWe present BiPON, an ontology integrating a multi-scale systemic representation of bacterial cellular processes. BiPON consists in of two sub-ontologies, bioBiPON and modelBiPON. bioBiPON organizes the systemic description of biological information while modelBiPON describes the mathematical models (including parameters) associated with biological processes. bioBiPON and modelBiPON are related using bridge rules on classes during automatic reasoning. Biological processes are thus automatically related to mathematical models. 37% of BiPON classes stem from different well-established bio-ontologies, while the others have been manually defined and curated. Currently, BiPON integrates the main processes involved in bacterial gene expression processes.ConclusionsBiPON is a proof of concept of the way to combine formally systems biology and bio-ontology. The knowledge formalization is highly flexible and generic. Most of the known cellular processes, new participants or new mathematical models could be inserted in BiPON. Altogether, BiPON opens up promising perspectives for knowledge integration and sharing and can be used by biologists, systems and computational biologists, and the emerging community of whole-cell modeling.

Developing an integrated framework for using data mining techniques and ontology concepts for process improvement

Process, as an important knowledge resource, must be effectively managed and improved. The main problems are the large number of processes, their specific features, and the complicated relationships between them, which all lead to the increase in complexity and create a high-dimensionality problem. Traditional process management systems are unable to manage and improve processes with a high volume of data. Data mining techniques, however, can be employed to identify valuable patterns. With the aid of these patterns, suggestions for process improvement can be presented. Further, process ontology can be applied to share the process patterns between people, facilitate the process understanding, and develop the reusability of the extracted patterns for process improvement.This study presents a combined three-part, five-stage framework of data mining, process improvement, and process ontology. To evaluate the applicability and effectiveness of the proposed framework, a real process dataset is applied. Two clustering and classification techniques are used to discover valuable patterns as the process ontology. The output of these two techniques can be considered as the recommendations for improving the processes. The proposed framework can be exploited to support process improvement methodologies in organizations.

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.

Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system

T-UCRs, a class of long non-coding RNAs that are transcribed from ultra-conserved regions (UCRs), might play an important role in development and diseases. However, the amount of T-UCRs that are conservatively expressed in the developing nervous systems of mice, monkeys and humans is still unknown. In this study, we screened the RNA sequence signals of 481 identified UCRs in an E14.5 mouse brain from the ENCODE database and found 76 UCRs that may be transcribed into T-UCRs. To verify the expression of these potential T-UCRs, we used an RT-PCR experiment and identified that 60 T-UCRs can be expressed in the E14.5 mouse brain. Furthermore, we detected the expression conservation of 76 potential T-UCRs in two comparisons: postnatal day 0 brains of a mouse and a rhesus monkey and neural stem cells of mouse and human by RT-PCR experimentation. It was found that up to 65% of these T-UCRs were expressed in mouse, rhesus monkey and human nervous systems. Next, by testing the spatiotemporal expression pattern of these T-UCRs expressed in mouse, rhesus monkey and human nervous systems, we found that approximately 30% of the T-UCRs showed a relatively high and dynamical expression during mouse brain development. Finally, through biological process and molecular function gene ontology analysis of the host genes of intronic or exonic-antisense T-UCRs, it was discovered that most of the genes were involved in RNA splicing or RNA binding. These results suggest that T-UCRs are likely to participate in nervous system development through RNA processing.

DNMT1 is associated with cell cycle and DNA replication gene sets in diffuse large B-cell lymphoma

Dysregulation of DNA (cytosine-5)-methyltransferase 1 (DNMT1) is associated with the pathogenesis of various types of cancer. It has been previously shown that DNMT1 is frequently expressed in diffuse large B-cell lymphoma (DLBCL), however its functions remain to be elucidated in the disease. In this study, we gene expression profiled (GEP) shRNA targeting DNMT1(shDNMT1)-treated germinal center B-cell-like DLBCL (GCB-DLBCL)-derived cell line (i.e. HT) compared with non-silencing shRNA (control shRNA)-treated HT cells. Independent gene set enrichment analysis (GSEA) performed using GEPs of shRNA-treated HT cells and primary GCB-DLBCL cases derived from two publicly-available datasets (i.e. GSE10846 and GSE31312) produced three separate lists of enriched gene sets for each gene sets collection from Molecular Signatures Database (MSigDB). Subsequent Venn analysis identified 268, 145 and six consensus gene sets from analyzing gene sets in C2 collection (curated gene sets), C5 sub-collection [gene sets from gene ontology (GO) biological process ontology] and Hallmark collection, respectively to be enriched in positive correlation with DNMT1 expression profiles in shRNA-treated HT cells, GSE10846 and GSE31312 datasets [false discovery rate (FDR) <0.05]. Cell cycle progression and DNA replication were among the significantly enriched biological processes (FDR <0.05). Expression of genes involved in the activation of cell cycle and DNA replication (e.g. CDK1, CCNA2, E2F2, PCNA, RFC5 and POLD3) were highly correlated (r>0.8) with DNMT1 expression and significantly downregulated (log fold-change <−1.35; p<0.05) following DNMT1 silencing in HT cells. These results suggest the involvement of DNMT1 in the activation of cell cycle and DNA replication in DLBCL cells.

An ontology-based approach supporting holistic structural design with the consideration of safety, environmental impact and cost

Early stage decision-making for structural design critically influences the overall cost and environmental performance of buildings and infrastructure. However, the current approach often fails to consider the multi-perspectives of structural design, such as safety, environmental issues and cost in a comprehensive way. This paper presents a holistic approach based on knowledge processing (ontology) to facilitate a smarter decision-making process for early design stage by informing designers of the environmental impact and cost along with safety considerations. The approach can give a reasoning based quantitative understanding of how the design alternatives using different concrete materials can affect the ultimate overall performance. Embodied CO2 and cost are both considered along with safety criteria as indicative multi-perspectives to demonstrate the novelty of the approach. A case study of a concrete structural frame is used to explain how the proposed method can be used by structural designers when taking multi performance criteria into account. The major contribution of the paper lies on the creation of a holistic knowledge base which links through different knowledge across sectors to enable the structural engineer to come up with much more comprehensive decisions instead of individual single objective targeted delivery.

Enabling supplier discovery through a part-focused manufacturing process ontology

ABSTRACTNumerous ontologies have been introduced to represent and activate engineering knowledge across the development process. However, many of the ontologies in the manufacturing domain provide limited usability for individuals who lack knowledge of manufacturing processes available within the domain. Similarly, web-based e-sourcing portals lack the ability to adequately pair components whose developers have limited knowledge of manufacturing processes with manufacturers who are able to produce their product. Motivated by these current gaps, an ontology is proposed which is designed to enable both users with a limited knowledge and those with a pre-existing knowledge of manufacturing to identify potential processes. The Part-focused Manufacturing Process Ontology is designed around the concept that manufacturing processes can be selected based upon desired features and attributes of a component/product. This differs from other ontologies that model the manufacturing process domain on the characteristics of the resources utilised in manufacturing. Further, the ontology is populated with some manufacturer data and its functionality demonstrated using component cases.

Expert system for nutrition care process of older adults

This paper presents an expert system for a nutrition care process tailored for the specific needs of elders. Dietary knowledge is defined by nutritionists and encoded as Nutrition Care Process Ontology, and then used as underlining base and standardized model for the nutrition care planning. An inference engine is developed on top of the ontology, providing semantic reasoning infrastructure and mechanisms for evaluating the rules defined for assessing short and long term elders’ self-feeding behaviours, to identify unhealthy dietary patterns and detect the early instauration of malnutrition. Our expert system provides personalized intervention plans covering nutrition education, diet prescription and food ordering adapted to the older adult’s specific nutritional needs, health conditions and food preferences. In-lab evaluation results are presented proving the usefulness and quality of the expert system as well as the computational efficiency, coupling and cohesion of the defined ontology.

Thinking in/through movements; Working with/in affect within the context of Norwegian early years education and practice

This paper draws on data undertaken with very young children within the context of Norwegian kindergartens. Specifically, the paper focuses on non-human and human movements. Mine included, that are undertaken in time and space. Following I argue that as the researcher I am always already entangled in inquiry and that there is no beginning. As a consequence, I cannot offer an account concerning movements that are predicated on humanist notions of linearity. Moreover, by immersing myself in process ontology, my efforts are not directed at using a presumed mastery where I both recognize and use a priori categories in order to render data intelligible and/or to reduce data to common sense. Rather, by paying careful attention to human and non-human bodies, and by being sensitive to and immersing myself within affect and movement, I draw attention to elements within the kindergarten which while, present are very often ignored by researchers and in so doing I disrupt traditional approaches to qualitative research. By effectively positioning myself in a post-human logic both the researcher and the research are open to different potentialities, potentialities where through thinking-feeling the peculiarities and differences of the empirical can be taken into account.

Personalized Identification of Differentially Expressed Modules in Osteosarcoma.

BackgroundOsteosarcoma (OS), an aggressive malignant neoplasm, is the most common primary bone cancer mainly in adolescents and young adults. Differentially expressed modules tend to distinguish differences integrally. Identifying modules individually has been crucial for understanding OS mechanisms and applications of custom therapeutic decisions in the future.Material/MethodsSamples came from individuals were used from control group (n=15) and OS group (n=84). Based on clique-merging, module-identification algorithm was used to identify modules from OS PPI networks. A novel approach – the individualized module aberrance score (iMAS) was performed to distinguish differences, making special use of accumulated normal samples (ANS). We performed biological process ontology to classify functionally modules. Then Support Vector Machine (SVM) was used to test distribution results of normal and OS group with screened modules.ResultsWe identified 83 modules containing 2084 genes from PPI network in which 61 modules were significantly different. Cluster analysis of OS using the iMAS method identified 5 modules clusters. Specificity=1.00 and Sensitivity=1.00 proved the distribution outcomes of screened modules were mainly consistent with that of total data, which suggested the efficiency of 61 modules.ConclusionsWe conclude that a novel pipeline that identified the dysregulated modules in individuals of OS. The constructed process is expected to aid in personalized health care, which may present fruitful strategies for medical therapy.

Universal History and the Emergence of Species Being

This paper seeks to recover the function of universal history, which was to place particulars into relation with universals. By the 20th century universal history was largely discredited because of an idealism that served to lend epistemic coherence to the overwhelming complexity arising from universal history's comprehensive scope. Idealism also attempted to account for history's being open - for the human ability to transcend circumstance. The paper attempts to recover these virtues without the idealism by defining universal history not by its scope but rather as a scientific method that provides an understanding of any kind of historical process, be it physical, biological or human. While this method is not new, it is in need of a development that offers a more robust historiography and warrant as a liberating historical consciousness. The first section constructs an ontology of process by defining matter as ontic probabilities rather than as closed entities. This is lent warrant in the next section through an appeal to contemporary physical science. The resulting conceptual frame and method is applied to the physical domain of existents, to the biological do - main of social being and finally to the human domain of species being. It is then used to account for the emergence of human history's initial stage - the Archaic Socio-Economic Formation and for history' stadial trajectory - its alternation of evolution and revolution.

Building business process ontology based on concept hierarchy model

The agility and efficiency of business processes have great influence on the company's competitiveness. However, current detection of business process management system reveals the problem that it does not satisfy the customer requirements, because there is a lack of sufficient semantic information between business process. This paper proposes an approach for ontology extraction on business process by incorporating concept hierarchy as background knowledge. Incorporating the background knowledge in procedure of the process ontology has two main advantages: 1) background knowledge accelerates the building process, thereby minimising the conversion cost; 2) background knowledge guides the extraction of knowledge, which hides in database. To validate the method given in this paper, we use part of the sales order processes from SAP reference process models to construct business process ontology. The gold standard experiments show using this method can correct an effective construct process ontology.

Towards a shared ontology: A generic classification of cognitive processes in conceptual design

Towards addressing ontological issues in design cognition research, this paper presents the first generic classification of cognitive processes investigated in protocol studies on conceptual design cognition. The classification is based on a systematic review of 47 studies published over the past 30 years. Three viewpoints on the nature of design cognition are outlined (search, exploration and design activities), highlighting considerable differences in the concepts and terminology applied to describe cognition. To provide a more unified view of the cognitive processes fundamentally under study, we map specific descriptions of cognitive processes provided in protocol studies to more generic, established definitions in the cognitive psychology literature. This reveals a set of 6 categories of cognitive process that appear to be commonly studied and are therefore likely to be prevalent in conceptual design: (1) long-term memory; (2) semantic processing; (3) visual perception; (4) mental imagery processing; (5) creative output production and (6) executive functions. The categories and their constituent processes are formalised in the generic classification. The classification provides the basis for a generic, shared ontology of cognitive processes in design that is conceptually and terminologically consistent with the ontology of cognitive psychology and neuroscience. In addition, the work highlights 6 key avenues for future empirical research: (1) the role of episodic and semantic memory; (2) consistent definitions of semantic processes; (3) the role of sketching from alternative theoretical perspectives on perception and mental imagery; (4) the role of working memory; (5) the meaning and nature of synthesis and (6) unidentified cognitive processes implicated in conceptual design elsewhere in the literature.

A systematic review of protocol studies on conceptual design cognition: Design as search and exploration

This paper reports findings from the first systematic review of protocol studies focusing specifically on conceptual design cognition, aiming to answer the following research question: What is our current understanding of the cognitive processes involved in conceptual design tasks carried out by individual designers? We reviewed 47 studies on architectural design, engineering design and product design engineering. This paper reports 24 cognitive processes investigated in a subset of 33 studies aligning with two viewpoints on the nature of designing: (V1) design as search (10 processes, 41.7%); and (V2) design as exploration (14 processes, 58.3%). Studies on search focused on solution search and problem structuring, involving: long-term memory retrieval; working memory; operators and reasoning processes. Studies on exploration investigated: co-evolutionary design; visual reasoning; cognitive actions; and unexpected discovery and situated requirements invention. Overall, considerable conceptual and terminological differences were observed among the studies. Nonetheless, a common focus on memory, semantic, associative, visual perceptual and mental imagery processes was observed to an extent. We suggest three challenges for future research to advance the field: (i) developing general models/theories; (ii) testing protocol study findings using objective methods conducive to larger samples and (iii) developing a shared ontology of cognitive processes in design.

FORMALIZATION OF DESCRIPTION OF TECHNOLOGICAL PROCESSES FOR MANUFACTURING OF MACHINE-BUILDING PARTS ON THE BASIS OF ONTOLOGY AND OBJECT-ORIENTED DATABASES

The article is devoted to the development of a structural representation of the technological processes of manufacturing machine-building parts on the basis of ontology and object-oriented databases. Based on the generality of the objectframe representation of knowledge for formal ontologies, and for object-oriented knowledge bases, an automated translation from the ontology language into object-oriented databases is considered using the ANTLR software tool. The ontology of technological processes in machine building is constructed on the basis of the analysis of the business process diagram of technology development and its decomposition. The ontology is represented in the RIF language, a kind of XML. A grammar of the RIF language and the EMITTER class have been created to generate code in the language of the object-oriented database db4o. Such a technique allows, when describing the technological process of manufacturing parts in the ontology language, to execute queries as methods of classes db4o, which reduces the time costs and improves the efficiency of such a combined system in comparison with the separate use of the editor OntoStudio or db4o..

Building business process ontology based on concept hierarchy model

Building business process ontology based on concept hierarchy model

Ontology-Driven Situation Assessment System Design and Development in IoT Domains

An ontology-driven approach to software design and development of situation assessment systems (SAS) for IoT applications is considered. As SAS is used to build the situational model for the external environment, it highly depends on the operational domain. To simplify the transition from the domain description to SAS dataflow process the ontology-driven approach is proposed. The main idea of the approach is to explicitly formalize SAS dataflow process in an ontological form. For this purpose, a domain-independent SAS ontology is proposed that allows automation of the dataflow process design. The dataflow process ontology is used to automate development and runtime stages of SAS lifecycle. The proposed ontology is included into the proposed instrument set. The set can be used to build SAS systems for different domains described with OWL ontology. The set is evaluated on a traffic control scenario.

The Unfortunate Misinterpretation of Miss Follett

Mary Follett was both a woman in public service in myriad roles from social worker to presidential advisor and a female public intellectual giving voice to what would later be called a feminist perspective. Based on a forthcoming book, this paper summarizes the fullness of Follett’s thinking and discusses the manner in which she is frequently misinterpreted in the literature, arguing that these misunderstandings are due to a lack of awareness of, or ability to grasp, her underlying relational process ontology. Misinterpretations in both the management and public administration literature are considered, ending with a call for scholars in both specializations to reconsider their interpretations from a more in-depth understanding of her work.

Bio-TDS: bioscience query tool discovery system.

Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 15 000 analytic tool descriptions integrated from well-established, community repositories. One of the primary components of the Bio-TDS is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS’s scientific impact was evaluated using sample questions posed by researchers retrieved from Biostars, a site focusing on biological data analysis. The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness. The Bio-TDS offers researchers the capacity to associate their bioscience question with the most relevant computational toolsets required for the data analysis in their knowledge discovery process.