Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products

Representing SNOMED CT Concept Evolutions using Process Profiles

Abstract. SNOMED CT is a very large biomedical terminology supported by a concept-based ontology. In recent years it has been distributed under the new release format 'RF2'. RF2 provides a more consistent and coherent mechanism for keeping track of changes over versions, even to the extent that -in theory at leastany release will contain enough information to allow reconstruction of all previous versions. In this paper, using the January 2016 release of SNOMED CT, we explore various ways to transform change-assertions in RF2 into a more uniform representation with the goal of assessing how faithful these changes are with respect to biomedical reality. Key elements in our approach are (1) recent proposals for the Information Artifact Ontology that provide a realism-based perspective on what it means for a representation to be about something, and (2) the expectation that the theory of what we call 'process profiles' can be applied not merely to quantitative information artifacts but also to other sorts of symbolic representations of processes

Warranted Diagnosis

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs

Ontologies relevant to behaviour change interventions: a method for their development.

Background: Behaviour and behaviour change are integral to many aspects of wellbeing and sustainability. However, reporting behaviour change interventions accurately and synthesising evidence about effective interventions is hindered by lacking a shared, scientific terminology to describe intervention characteristics. Ontologies are standardised frameworks that provide controlled vocabularies to help unify and connect scientific fields. To date, there is no published guidance on the specific methods required to develop ontologies relevant to behaviour change. We report the creation and refinement of a method for developing ontologies that make up the Behaviour Change Intervention Ontology (BCIO). Aims: (1) To describe the development method of the BCIO and explain its rationale; (2) To provide guidance on implementing the activities within the development method. Method and results: The method for developing ontologies relevant to behaviour change interventions was constructed by considering principles of good practice in ontology development and identifying key activities required to follow those principles. The method's details were refined through application to developing two ontologies. The resulting ontology development method involved: (1) defining the ontology's scope; (2) identifying key entities; (3) refining the ontology through an iterative process of literature annotation, discussion and revision; (4) expert stakeholder review; (5) testing inter-rater reliability; (6) specifying relationships between entities, and; (7) disseminating and maintaining the ontology. Guidance is provided for conducting relevant activities for each step.  Conclusions: We have developed a detailed method for creating ontologies relevant to behaviour change interventions, together with practical guidance for each step, reflecting principles of good practice in ontology development. The most novel aspects of the method are the use of formal mechanisms for literature annotation and expert stakeholder review to develop and improve the ontology content. We suggest the mnemonic SELAR3, representing the method's first six steps as Scope, Entities, Literature Annotation, Review, Reliability, Relationships

Ontologies relevant to behaviour change interventions: a method for their development [version 2; peer review: 1 not approved]

Background: Behaviour and behaviour change are integral to many aspects of wellbeing and sustainability. However, reporting behaviour change interventions accurately and synthesising evidence about effective interventions is hindered by lacking a shared, scientific terminology to describe intervention characteristics. Ontologies are knowledge structures that provide controlled vocabularies to help unify and connect scientific fields. To date, there is no published guidance on the specific methods required to develop ontologies relevant to behaviour change. We report the creation and refinement of a method for developing ontologies that make up the Behaviour Change Intervention Ontology (BCIO). / Aims: (1) To describe the development method of the BCIO and explain its rationale; (2) To provide guidance on implementing the activities within the development method. / Method and results: The method for developing ontologies relevant to behaviour change interventions was constructed by considering principles of good practice in ontology development and identifying key activities required to follow those principles. The method’s details were refined through application to developing two ontologies. The resulting ontology development method involved: (1) defining the ontology’s scope; (2) identifying key entities; (3) refining the ontology through an iterative process of literature annotation, discussion and revision; (4) expert stakeholder review; (5) testing inter-rater reliability; (6) specifying relationships between entities, and; (7) disseminating and maintaining the ontology. Guidance is provided for conducting relevant activities for each step. / Conclusions: We have developed a detailed method for creating ontologies relevant to behaviour change interventions, together with practical guidance for each step, reflecting principles of good practice in ontology development. The most novel aspects of the method are the use of formal mechanisms for literature annotation and expert stakeholder review to develop and improve the ontology content. We suggest the mnemonic SELAR3, representing the method’s first six steps as Scope, Entities, Literature Annotation, Review, Reliability, Relationships

A black art: Ontology, data, and the Tower of Babel problem

Computational ontologies are a new type of emerging scientific media (Smith, 2016) that process large quantities of heterogeneous data about portions of reality. Applied computational ontologies are used for semantically integrating (Heiler, 1995; Pileggi & Fernandez-Llatas, 2012) divergent data to represent reality and in so doing applied computational ontologies alter conceptions of materiality and produce new realities based on levels of informational granularity and abstraction (Floridi, 2011), resulting in a new type of informational ontology (Iliadis, 2013) the critical analysis of which requires new methods and frameworks. Currently, there is a lack of literature addressing the theoretical, social, and critical dimensions of such informational ontologies, applied computational ontologies, and the interdisciplinary communities of practice (Brown & Duguid, 1991; Wenger, 1998) that produce them. This dissertation fills a lacuna in communicative work in an emerging subfield of Science and Technology Studies (Latour & Woolgar, 1979) known as Critical Data Studies (boyd & Crawford, 2012; Dalton & Thatcher, 2014; Kitchin & Lauriault, 2014) by adopting a critical framework to analyze the systems of thought that inform applied computational ontology while offering insight into its realism-based methods and philosophical frameworks to gauge their ethical import. Since the early 1990s, computational ontologies have been used to organize massive amounts of heterogeneous data by individuating reality into computable parts, attributes, and relations. This dissertation provides a theory of computational ontologies as technologies of individuation (Simondon, 2005) that translate disparate data to produce informational cohesion. By technologies of individuation I mean engineered artifacts whose purpose is to partition portions of reality into computable informational objects. I argue that data are metastable entities and that computational ontologies restrain heterogeneous data via a process of translation to produce semantic interoperability. In this way, I show that computational ontologies effectively re-ontologize (Floridi, 2013) and produce reality and thus that have ethical consequences, specifically in terms of their application to social reality and social ontology (Searle, 2006). I use the Basic Formal Ontology (Arp, Smith, & Spear, 2015)—the world’s most widely used upper-level ontology—as a case study and analyze its methods and ensuing ethical issues concerning its social application in the Military Ontology before recommending an ethical framework. “Ontology” is a term that is used in philosophy and computer science in related but different ways—philosophical ontology typically concerns metaphysics while computational ontology typically concerns databases. This dissertation provides a critical history and theory of ontology and the interdisciplinary teams of researchers that came to adopt methods from philosophical ontology to build, persuade, and reason with applied computational ontology. Following a critical communication approach, I define applied computational ontology construction as a solution to a communication problem among scientists who seek to create semantic interoperability among data and argue that applied ontology is philosophical, informational in nature, and communicatively constituted (McPhee & Zaug, 2000). The primary aim is to explain how philosophy informs applied computational ontology while showing how such ontologies became instantiated in material organizations, how to study them, and describe their ethical implications

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

A framework for analyzing changes in health care lexicons and nomenclatures

Ontologies play a crucial role in current web-based biomedical applications for capturing contextual knowledge in the domain of life sciences. Many of the so-called bio-ontologies and controlled vocabularies are known to be seriously defective from both terminological and ontological perspectives, and do not sufficiently comply with the standards to be considered formai ontologies. Therefore, they are continuously evolving in order to fix the problems and provide valid knowledge. Moreover, many problems in ontology evolution often originate from incomplete knowledge about the given domain. As our knowledge improves, the related definitions in the ontologies will be altered. This problem is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations, and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies, and interactions with other existing ontologies have been widely neglected. In this research, alter revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, RLR (Represent, Legitimate, and Reproduce), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general, and aids in tracking and representing the changes, particularly through the use of category theory. Category theory has been used as a mathematical vehicle for modeling changes in ontologies and representing agents' interactions, independent of any specific choice of ontology language or particular implementation. We have also employed rule-based hierarchical graph transformation techniques to propose a more specific semantics for analyzing ontological changes and transformations between different versions of an ontology, as well as tracking the effects of a change in different levels of abstractions. Thus, the RLR framework enables one to manage changes in ontologies, not as standalone artifacts in isolation, but in contact with other ontologies in an openly distributed semantic web environment. The emphasis upon the generality and abstractness makes RLR more feasible in the multi-disciplinary domain of biomedical Ontology change management

Toward the use of upper level ontologies for semantically interoperable systems: an emergency management use case

In the context of globalization and knowledge management, information technologies require an ample need of unprecedented levels of data exchange and sharing to allow collaboration between heterogeneous systems. Yet, understanding the semantics of the exchanged data is one of the major challenges. Semantic interoperability can be ensured by capturing knowledge from diverse sources by using ontologies and align these latter by using upper level ontologies to come up with a common shared vocabulary. In this paper, we aim in one hand to investigate the role of upper level ontologies as a mean for enabling the formalization and integration of heterogeneous sources of information and how it may support interoperability of systems. On the other hand, we present several upper level ontologies and how we chose and then used Basic Formal Ontology (BFO) as an upper level ontology and Common Core Ontology (CCO) as a mid-level ontology to develop a modular ontology that define emergency responders’ knowledge starting from firefighters’ module for a solution to the semantic interoperability problem in emergency management

Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński