Ontological Infrastructure Research Articles

Infrastructuring Educational Genomics: Associations, Architectures, and Apparatuses

AbstractTechnoscientific transformations in molecular genomics have begun to influence knowledge production in education. Interdisciplinary scientific consortia are seeking to identify ‘genetic influences’ on ‘educationally relevant’ traits, behaviors, and outcomes. This article examines the emerging ‘knowledge infrastructure’ of educational genomics, attending to the assembly and choreography of organizational associations, epistemic architecture, and technoscientific apparatuses implicated in the generation of genomic understandings from masses of bioinformation. As an infrastructure of datafied knowledge production, educational genomics is embedded in data-centered epistemologies and practices which recast educational problems in terms of molecular genetic associations—insights about which are deemed discoverable from digital bioinformation and potentially open to genetically informed interventions in policy and practice. While scientists claim to be ‘opening the black box of the genome’ and its association with educational outcomes, we open the black box of educational genomics itself as a source of emerging scientific authority. Data-intensive educational genomics does not straightforwardly ‘discover’ the biological bases of educationally relevant behaviors and outcomes. Rather, this knowledge infrastructure is also an experimental ‘ontological infrastructure’ supporting particular ways of knowing, understanding, explaining, and intervening in education, and recasting the human subjects of education as being surveyable and predictable through the algorithmic processing of bioinformation.

Working for the Invisible Machines or Pumping Information into an Empty Void? An Exploration of Wikidata Contributors' Motivations

Structured data peer production (SDPP) platforms like Wikidata play an important role in knowledge production. Compared to traditional peer production platforms like Wikipedia, Wikidata data is more structured and intended to be used by machines, not (directly) by people; end-user interactions with Wikidata often happen through intermediary "invisible machines." Given this distinction, we wanted to understand Wikidata contributor motivations and how they are affected by usage invisibility caused by the machine intermediaries. Through an inductive thematic analysis of 15 interviews, we find that: (i) Wikidata editors take on two archetypes---Architects who define the ontological infrastructure of Wikidata, and Masons who build the database through data entry and editing; (ii) the structured nature of Wikidata reveals novel editor motivations, such as an innate drive for organizational work; (iii) most Wikidata editors have little understanding of how their contributions are used, which may demotivate some. We synthesize these insights to help guide the future design of SDPP platforms in supporting the engagement of different types of editors.

Stranger Things, Plant Life, and Posthuman Endgames: Reading Beckett with Others

This essay reads work by Samuel Beckett, especially his prose, with a focus on vegetal ontology and plant life, soil, mud, and dirt. By juxtaposing Beckett with recent fiction, e.g., the Netflix series Stranger Things, contemporary plant theory, and the general ecology of Erich Hörl, posthuman entanglements and relations are discussed as part of an ontological infrastructure in the texts, which can also be linked to Beckett’s interest in prosthetics and technical media. It is suggested that an approach of this kind might offer new perspectives on the dispersed subjectivity in Beckett’s texts.

A Divine Rebellion: Indigenous Sacraments among Global “Lamanites”

This essay engages with some of the experiences and metaphysics of Indigenous peoples who are members of The Church of Jesus Christ of Latter-day Saints (Mormonism/LDS/the Church) by responding to their structural construction as “Lamanites”. Lamanites have been interpreted within Mormonism to be ancestors of various global Indigenous peoples of the “Americas” and “Polynesia”. This essay reveals how contemporary Indigenous agency by presumed descendants of the Lamanites, who embrace both an Indigenous and a Mormon identity, shifts the cosmology of the Church. Interpretations of TheBook of Mormon that empower contemporary Indigenous agency paradoxically materialize a divinely inspired cultural rebellion within the Church itself. However, this tension that is mediated by Lamanites in the Church is not framed as an exclusive response to the Church itself but, rather, to a larger global hegemony of coloniality to which the Church is subject. These Lamanite worldviews can be understood as a process of restoring ancestral Indigenous sacraments (rituals) through Mormon paradigms, which are found and nurtured in the cracks and fissures of both the material and ontological infrastructure of Mormonism’s dominant paradigm. When Indigenous Mormons assert autonomous authorship of their own cosmogony and metaphysics, the Church beliefs of restoring a ‘primitive Christian church’ and ‘becoming Gods’ is creatively transformed into a more relevant and liberating possibility here and now.

Top-Down and Bottom-Up Legal System as a Gödel Machine With Object-Oriented Framework

The past decade has witnessed the exponential growth of data-driven industrial revolutions, from e-commerce to the internet of things (IoT), and from social media to its notorious abuses. A similar albeit milder trend is swiping across the landscape of the legal profession has experienced the radical changes brought by advancements in Artificial Intelligence (“AI”) in recent years. There were two dominant approaches to digitally represent the legal reasoning: the top-down approach where legal experts were engaged to analyze and design the legal system by its operational parts, while in contrast, the bottom-up approach uses machine learning to build up models for legal reasoning from the decided cases. the top-down approach focuses on representing the domain knowledge into Ontological Structures that can be better communicated to the computer scientist in a CRISP-DM cycle. Top-down approach has long been employed in the legal profession to communicate legal concepts and logic relationships concisely and precisely. Vigorous attempts have been made to translate natural-language-based legal texts into machine-readable (executable) versions through tools such as Ontology Web Language (OWL). The top-down approach, despite its conceptual simplicity and clarity, suffers from a significate drawback: knowledge acquisition bottleneck, that that it is expensive to create, maintain and update such system. On the other hand, the bottom-up approach has been taking the headlines in recent years with vendors of legal analytic products that allegedly beaten the best lawyers in legal analysis for the specialized domain of the law while charging a fraction of the fee. However, one must stop to ponder upon what stands behind the miraculous veil of the technological black box: the irresistible temptation to improve the predictive accuracy, and when the algorithm runs out of permissible, admissible, and legal material of a case, it embarks on extraneous factors: parties, their lawyers, judges, and even judge’s breakfasts, which are the “prohibited zone of reasoning” that the law consistently seeks to outlaw. In light of the ambitious progress to digitize the law, some normative and doctrinal controls must be in place to ensure that the learning programs do not merely learn from whatever the past offers but learn the desirable normative values as we aspire to enshrine in our legal systems. This paper, therefore, seeks to establish the fabrics of a framework that represents legal system using autopoiesis system conception top-down while building up the ontological infrastructure with Object-Method-Property model bottom-up, which may together serve as a useful bridge between the two dominate approaches while maintaining the legal system as we know it. This paper will start top-down by discussing the system dynamics of the law as a self-reproducing self-referential closed autopoiesis social system and then advances to analyze Godel Machine concept (“GM”) in computer science may be employed to digitally re-produce the organics of the law as a social system. Then, this paper will present some fundamentals of the Object-oriented programming (“OOP”) paradigm and how its inherent similarity to the legal reasoning forms the foundation to fit the building stocks from existing legal materials bottom-up into the scaffold of the system of law designed top-down. A line must be drawn between the part of the law that should be built top-down and the part bottom-up. The importance of maintaining a human-centred top layer of the law and the benefit of automating the lower layers through machine learning must be balanced. The OOP-GM model could have multiple benefits. First, it can maintain the adaptivity of the legal system to social changes while consistently enforcing normative expectations. Second, the OOP-GM offers a comprehensive model of ontological construction of legal concepts while maintaining compatibility to integrate with most objected-reoriented programming languages. Thirdly, OOP-GM offers greater analytical precision for the communication of law which provides for greater general access to the law as well as structural clarity for legal drafting, practices, and education. Lastly, machine learning functions with specific control on the input parameters is very unlikely to be influenced by extraneous factors, which provides for greater fairness and confidence in the legal system.

The Ends of Autotheory

The Ends of Autotheory Che Gossett (bio) Endings I'm always looking for terms that are not "memoir" to describe autobiographical writing that exceeds the boundaries of the "personal." —Maggie Nelson1 I have written then what is meant to be not so much my autobiography as the autobiography of a concept of race. —W. E. B. Du Bois2 What is the relationship between autotheory, blackness, and abolition? Where does the autobiographical end and autotheory begin? What is the relationship between the autobiography of the concept of race and personhood? Between autotheory and the autotelic? What does the notion of the self as a possessive property have to do with the carceral metaphysics of the subject? Saidiya Hartman's critical labors on and ever urgent diagnosis of slavery and freedom's historical and contemporary, political, and ontological "double bind" are a condition of possibility for such questions and abolitionist aporias.3 Not aporias, however, in the sense of an unsurpassable impasse or foreclosure to which we must surrender. In his seminars on the death penalty and abolition, Jacques Derrida argued against the carceral conception of the impasse as "a prison," resisting the predominant figuration of the aporetic as "what stops or arrests, often in the form of a judgement or verdict."4 Rather than a deadlock, an aporia, then, might be seen as a threshold. In this brief reflection, I follow the piercing insights of blackness as identity's critique. By identity's critique, I mean the way in which blackness explodes what Frank Wilderson so aptly calls the "assumptive logic" undergirding the aesthetic, political, philosophical, and ontological edifice of the human and the predicates of personhood.5 Poet and critical scholar Fred Moten profoundly and beautifully invites all into the fold of the "ensemblic" (inter)play of "study."6 I turn toward the shimmering illuminations within and the lifelong (and life-exceeding) thought of Sylvia Wynter, Katherine McKittrick, Hortense Spillers, Saidiya Hartman, W. E. B. Du Bois, George L. Jackson, Cedric Robinson, Brent Hayes Edwards, Fred Moten, Laura Harris, R. A. Judy, and M. NourbeSe Philip. Blackness not only exceeds the boundaries of the personal but problematizes the category of personhood itself. I touch on moments where the consonance of the self is rendered dissonant and problematized under the critical analysis of blackness's relation to the human and being. The aesthetic-political and ontological infrastructure of the self is jolted, short-circuited by another frequency of thought: a live wire. [End Page 577] And notice! One major implication here: humanness is no longer a noun. Being human is a praxis. —Sylvia Wynter7 Sylvia Wynter has dedicated her synoptic, capacious, generative, and generous brilliance to not only diagnosing the human as a genre of the racial but also through and as that critical labor, an outside: praxis. This is made available through the generosity of thought shared between Wynter and editor Katherine McKittrick in the phenomenal 2015 anthology that both gathers and is a gathering—in the sense of celebration and engagement—for her remarkable work.8 Wynter's work is also an indispensable contribution to philosophy of mind and interrogates the very premises and grammar of that disciplinary formation. She shows how the genre of Man and all its predicates, including mind, are part of a racial and colonial episteme. Wynter deviates from functionalism, which posits that mind is purely its operations, and instead argues for the primacy of sociogenesis: "if the mind is what the brain does, what the brain does, is itself culturally determined through the mediation of the socialized sense of self, as well of the 'social' situation in which this self is placed."9 Mind as neurology's warden, the executive function as precinct. Wynter's approach thinks the sociality of mind, as opposed to its ipseity. The neurocentric figuration of the self is demystified and denaturalized. Swarm W.E.B. Du Bois's Black Reconstruction in America, first published in 1935, is a required text and fundamental touchstone for the study and theory of abolition. In this paradigmaltering work, Du Bois enacts an epistemic break with the historiography of the Civil War of his time and shows how Black struggle—via...

Robust Evolution in Historical Time

The normalized, deterministic conception of evolution espoused by Dennett is increasingly being challenged by theorists who, following Gould, emphasize the role that historical contingencies play in it. I explore the conflict between these views and argue that correcting our understanding of the relationship between nature’s systematic necessities and historical temporality can resolve it. The mathematically precise laws science formulates describe the systematic patterns of nature abstractly and, as abstractions, these laws do not preclude but allow for the contingencies of historical time. Drawing on Heidegger and Hume, I argue that historical time is characterized by the ingression of the unprecedented future into the present. This is the ontological infrastructure that makes the evolution of unprecedented ontological alterities possible.

A Fuzzy Ontological Infrastructure for Semantic Interoperability in Distributed Electronic Health Record

A Fuzzy Ontological Infrastructure for Semantic Interoperability in Distributed Electronic Health Record

Practice-based ontological design for multiplying realities

This text argues that a practice-based notion of ontological design is useful for designers to transform the politics of the already designed world. The text analyzes three approaches to the philosophical concept of ontology and suggests that a Science and Technology Studies approach focused on observing ontologies in practice provides pragmatic potential for designers to intervene in public controversies. The author's case study of a contested airport expansion demonstrates that this approach can sensitize the designer to multiple realities, identify 'where' the ontological infrastructure of a problem is located, and define 'what' design is needed to transform a controversy. The text uses these findings to propose principles of practice-based ontological design that can support designers who are seeking to transform the world into a series of situated controversies.

Towards an ontological infrastructure for chemical process simulation and optimization in the context of eco-industrial parks

In this paper, we introduce the concept of constructing an ontology-based decision support system called J-Park Simulator for the design and operation of eco-industrial parks. It is inspired by Jurong industrial park in Singapore. A biodiesel plant is implemented into the system as a first step. OntoCAPE is adapted for the purposes of the biodiesel plant to establish a knowledge base, which is employed to carry out a number of applications via J-Park Simulator. Firstly, information query can be performed. Information of the biodiesel plant can be extracted through natural language query. Secondly, J-Park Simulator can be used to carry out process simulation. New process equilibrium can be evaluated after certain operation parameters change. Thirdly, process optimization can be realized through J-Park Simulator. Optimal operation condition under different market scenarios can be obtained for the biodiesel producing process in order to reduce the energy consumption and achieve maximal plant profit.

English

English

Upgrade of a current research information system with ontologically supported semantic search engine

Harmonising the metadata format alone does not solve the issue of efficient access to relevant information in heterogeneous environments, when different systems use different content, contextual and semantic concepts for certain entities. One such type of heterogeneous systems are also Current Research Information Systems (CRIS), which store their data primarily in local relational databases, using different formats and various local concepts.In this article, we study the possibilities and propose a new ontologically supported semantic search engine (OSSSE) which, in addition to the harmonisation of the metadata format among local CRIS systems, also ensures that the meaning of data and/or concepts that belong to various metadata entities are also harmonised. A special model of ontological infrastructure was designed, and dedicated test ontology was created alongside with a new simplified algorithm for creating ontology, the basis of which is the distinction between new and already existing classes in terms of content. Finally, we evaluated the proposed OSSSE model using a simulation of the search process on the base of 41,113 real searches within SICRIS. The obtained results show that regardless of the search situation, the proposed OSSSE is always at least as efficient as a search without ontological support in terms of precision, while recall remains the same; the improvement has been shown to be statistically significant with a high confidence interval (p<0.005).The proposed OSSSE model is able to solve the issue of harmonizing the data where different heterogeneous systems use different content, contextual and semantic concepts, which is the case in many advanced expert systems. In this manner, the more the search is carried out based on the properties described by the supporting ontology, the more the infrastructure can help a searcher. The proposed concepts, ontological infrastructure and the designed semantic search engine may well help to improve search precision in several information retrieval systems.

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

BackgroundBiomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats.MethodsWe present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes.ResultsThe results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned.ConclusionsWe have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.

An ISO-based software process ontology pattern language and its application for harmonizing standards

Many efforts have been made for modeling and standardizing software processes. ISO/IEC JTC1/SC7, the ISO sub-committee responsible for software and systems engineering, is one of the most important groups devoted to this task. However, standards developed by this committee are frequently inconsistent and even contradictory. This led to the need for an ISO Study Group to investigate the creation of an ontological infrastructure to establish a common conceptualization for underpinning all SC7 standards. This ISO initiative is a work in progress, which has focused on the software process domain and, in particular, considering the ISO/IEC 24744 standard. In this paper, we advocate in favor of using an Ontology Pattern Language (OPL) as the main component of this ontological infrastructure. We present ISP-OPL (ISO-based Software Process OPL), an OPL that can be applied as a basis for harmonizing software process-related ISO standards, favoring reuse when building aligned specific software process ontologies for Software Engineering sub-domains. In order to evaluate its applicability, we conducted an experiment involving seven domain ontologies, developed using ISP-OPL.

An ontology for ISO software engineering standards: 1) Creating the infrastructure

Software engineering standards developed under the auspices of ISO/IEC JTC1's SC7 have been identified as employing terms whose definitions vary significantly between standards. This led to a request in 2012 to investigate the creation of an ontological infrastructure that aims to be a single coherent underpinning for all SC7 standards, present and future. Here, we develop that necessary infrastructure prior to its adoption by SC7 and its implementation (likely 2014). The proposal described here requires, firstly, the identification of a single comprehensive set of definitions, the definitional elements ontology (DEO). For the scope of an individual standard, only a subset of these definitional elements will be needed. Once configured, this definitional subset creates a configured definitional ontology or CDO. Both the DEO and the CDO are essentially foundational ontologies from which a domain-specific ontology known as a SDO or standard domain ontology can be created. Consequently, all such SDOs are conformant to a CDO and hence to the single DEO thus ensuring that all standards use the same ontological base. Standards developed in this fashion will therefore be not only of a higher quality but also, importantly, interoperable.

Linking Genome Annotation Projects with Genetic Disorders using Ontologies

Genome sequencing projects generate vast amounts of data of a wide variety of types and complexities, and at a growing pace. Traditionally, the annotation of such sequences was difficult to share with other researchers. Despite the fact that this has improved with the development and application of biological ontologies, such annotation efforts remain isolated since the amount of information that can be used from other annotation projects is limited. In addition to this, they do not benefit from the translational information available for the genomic sequences. In this paper, we describe a system that supports genome annotation processes by providing useful information about orthologous genes and the genetic disorders which can be associated with a gene identified in a sequence. The seamless integration of such data will be facilitated by an ontological infrastructure which, following best practices in ontology engineering, will reuse existing biological ontologies like Sequence Ontology or Ontological Gene Orthology.

Towards an ontological infrastructure for chemical batch process management

A crucial step for batch process improvement and optimization is to develop information structures that streamline data gathering and, above all, are capable of integrating transactional data into a system using the analytical tools that are developed. Current trends in electronics, computer science, artificial intelligence and control system technology are providing technical capability that greatly facilitates the development of multilevel decision-making support. In this paper, we present the batch process ontology (BaPrOn), wherein different concepts regarding batch processes are categorized and the relationships between them are examined and structured in accordance with ANSI/ISA-88 standards, which provide a solid and transparent framework for integrating batch-related information. This paper also focuses on systematic integration of different actors within the control process. The proposed approach bases the conceptualization through the ANSI/ISA-88 representation, providing the advantage of establishing a more general conceptualization of the batch process domain. The capabilities of the envisaged ontological framework were assessed in a test bed PROCEL pilot plant: scheduling-monitoring and control-rescheduling was closed, information quality was accessed by knowledge description, and an optimum decision-making task was performed. The ontological structure can be extended in the future to incorporate other hierarchical levels and their respective modeling knowledge.

An ontological framework for automated regulatory compliance in pharmaceutical manufacturing

Pharmaceutical manufacture is one of the most tightly legislated industries today. The industry is constantly challenged to meet the rising standards of manufacturing quality and safety through rigorous regulatory requirements. As a consequence, ensuring regulatory compliance and managing a myriad of validation documents constitutes a major informatics challenge. This study addresses this challenge by developing an ontological infrastructure to support decision making in regulatory compliance. The proposed ontological informatics system, called OntoReg, is integrated with a reasoner and a rule engine through a Java integrated development environment. The system is demonstrated through industrial case studies based on regulation examples taken from the Eudralex Guide 2007.

A semantic-based framework for multimedia management and interoperability

Interoperable, semantic-based audiovisual content services are necessary in the open Internet environment, where the volume of the available audiovisual information is growing rapidly. Such services can be built on top of structured, semantic-based audiovisual content descriptions. This thesis focuses on the representation and management of the audiovisual content semantics. The representation and management of the audiovisual content semantics are based on the dominant standards for audiovisual content description and ontology representation which are, respectively, the MPEG-7 and the OWL. In particular, the following components have been developed for the representation and management of the audiovisual content semantics: • An MPEG-7 based model that allows: (a) The representation of the audiovisual content semantics; and (b) The representation of domain ontologies that extend the generalpurpose MPEG-7 semantics with domain knowledge and may be utilized in the audiovisual content description. • An ontological infrastructure, which allows the representation and management of the audiovisual content semantics. This ontological infrastructure represents the MPEG-7 semantics and allows their extension with application-specific and domain-specific knowledge. • A mapping model that allows interoperability support between MPEG-7 and OWL. This model maps the MPEG-7 constructs to OWL constructs and allows the transformation of OWL domain ontologies and OWL/RDF audiovisual content descriptions into MPEG-7 descriptions.

How a philosophical theory of causation may help in ontological engineering

The Institute for Formal Ontology and Medical Information Science, IFOMIS (http://ifomis.de) at the University of Leipzig, is developing a common reference ontology for the medical domain. This ontology will be developed in tandem with work on ontology formalization being carried out at the Universities of Leeds (http://www.comp.leeds.ac.uk/ brandon/ontology/) and Trento and Rome (http:// ontology.ip.rm.cnr.it/) and elsewhere. It will also provide part of the ontological infrastructure for the systems for the extraction of digitalized information content from unstructured medical text that are being developed in Belgium by the company Language and Communication NV (http://www. landc.be). Whilst the technology for running databases has reached an impressive state of maturity, the classification systems upon which this technology is based are the products of myriad ad hoc decisions stretching back to the early days of database design. The resulting inadequacies become apparent, for example, wherever attempts are made to integrate data from different sources. The problems remind one of the old fable of the Tower of Babel. A central classification system designed to facilitate database integration was called by information scientists an ‘ontology’. At IFOMIS we assume that the 2000 year-old philosophical discipline that is traditionally called ‘ontology’ is vital for the kind of ontology information scientists are developing. Since Aristotle’s day, philosophers have been working on many of the problems that underlie the problems ontological engineers are working on. Examples of such problems concern universals and particulars, properties and relations, events and processes. At IFOMIS we assume that for building ontologies we need true philosophical theories about reality, rather than just representations of concepts or beliefs. My purpose here is to illustrate this claim by explaining how a philosophical theory of causation may help in ontological engineering.