Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant (...) to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable (...) strategy for the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Standpoint epistemology has been linked with increasing calls for deference to the socially marginalized. As we understand it, deference involves recognizing someone else as better positioned than we are, either to investigate or to answer some question, and then accepting their judgment as our own. We connect contemporary calls for deference to old objections that standpoint epistemology wrongly reifies differences between groups. We also argue that while deferential epistemic norms present themselves as a solution to longstanding injustices, habitual deference prevents (...) the socially dominant from developing for themselves the skills necessary to expand their capacity for empathy, to deftly probe for evidence, and to ask critical questions. Consequently, we argue that standpoint epistemology must be understood as calling for inclusion, not deference. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is (...) designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and (...) familiarizing the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

This is a commentary on the article by Augusto (2022; this issue) on categories and foundation ontology (FO). We agree that the notion of categories of kinds of elements to devise a FO deserves more attention than it has received to date. From a practical point of view sensu developing domain ontologies, however, it probably does not matter much as long as a FO is used and that that one was understood.

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

Words are indispensable linguistic tools for beings like us. However, there is not much philosophical work done about what words really are. In this paper, I develop a new ontology for words. I argue that words are abstract artifacts that are created to fulfill various kinds of purposes, and words are abstract in the sense that they are not located in space but they have a beginning and may have an end in time given that certain conditions are (...) met. What follows from this two-fold argument is that words, from an ontological point of view, are more like musical works, fictional characters or computer programs, than numbers or sets. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On (...) the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by (...) taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use (...) ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set (...) of principles learned from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the (...) anthropic principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...) by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational (...) modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in (...) a variety of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) should be considered not as restricted to Substantial types but instead should be applied to model Endurant Types in general, including Relator types, Quality types and Mode types. We also contribute a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, and (...) mapped to the ontology of time. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General (...) Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned (...) in the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop (...) and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the (...) view of brands as mere marks or names and interpret them as emergent products with properties that afford branding in the sense of Gibson’s ecological psychology. Brand strength is a function of the degree to which brands occupy defensible niches in product space. Branding as a process involves changing external or internal boundaries of products. Several arguments are proposed in favor of brand realism. The fragments of an ontology of marketing are developed in a broadly Aristotelian framework. Brand realism has significant implications for a new understanding of issues ranging from the effects of advertising to financial brand valuation, the nature of trademarks, and marketing strategy in general. It permits one to treat brand equity as a real phenomenon not dependent on associations, attitudinal states such as brand loyalty, or spurious constructs such as brand character or personality. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult (...) to extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Objective – is to formulate a methodological discourse regarding the place and role of the language interconnected with the process of socialization of a person and develop a systemic idea of the corresponding functional features. -/- Materials & Methods – this discourse is formulated on the basis of a systemic idea of the personality socialization, which, in turn, is realized using the structural-ontological method of studying the subject matter field in interdisciplinary researches. This method involves the construction of special visual-graphic (...) matrices that reflect the interaction of the primary process and the material of the studied system. -/- Results. The work with the structural-ontological matrix made it possible to analyze the functions of the language in the context of such significant factors of socialization as complex psychodynamics, civilization space and the function of reflection. At the same time, reflection is considered at the level of two plans – primary (reflection-bond) and secondary (reflection-splitting). This made it possible to deduce the idea of the role of language beyond the traditional framework of working with text and analyze the place of the language in the context of activities to establish a connection between individuals, which is realized in a specific cooperative situation (Shchedrovitsky). In particular, the look at language as a specific tool of civilizational rationing, the mechanism of which is provided through reflection-communication. Thus, the language is examined through the prism of its systemic influence on the morphology of the psyche. -/- Conclusions – a structural-ontological analysis of the place and role of language in the process of personality socialization has led us to construction of a hypothesis about the phenomenon of language discontentment, as a tendency to distance away ego-consciousness in the process of individuation from linguistic ontology. The arguments were also advanced in favor of the assumption regarding the peculiarities of the influence of language discontentment on cultural activities and the psychodynamic contribution of this phenomenon in the midlife crisis (Jung). (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

This paper aims to evidence the meaning of “ontology of present”, a concept elaborated by Michel Foucault, and intends to elucidate the philosopher’s idea that subjectivity is historically formed. The context of the concept’s emergence will be analyzed, considering Foucault’s studies on the ancient greco-roman moral, in which he discuss the role of liberty and autonomy in the development of citizens. To the philosopher, the ontology of present consists in a critic of the domination and subjugation mechanisms, (...) produced by disciplinary and control societies. With this critic, Foucault pictures theoric tools to analyze the actuality, making possible to transform the historical processes of subjectification. Keywords: ontology of the present; subjectivity; history; Michel Foucault; actuality. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop (...) and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...) on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain. (shrink)

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which (...) may however provide general lessons for the developers of ontologies in the future. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, (...) agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Developing tools is a crucial aspect of experimental practice, yet most discussions of scientific change traditionally emphasize theoretical over technological change. To elaborate on the role of tools in scientific change, I offer an account that shows how scientists use tools in exploratory experiments to form novel concepts. I apply this account to two cases in neuroscience and show how tool development and concept formation are often intertwined in episodes of tool-driven change. I support this view (...) by proposing common normative principles that specify when exploratory concept formation and tool development succeed to initiate scientific change. (shrink)

This paper is concerned with certain ontological issues in the foundations of geographic representation. It sets out what these basic issues are, describes the tools needed to deal with them, and draws some implications for a general theory of spatial representation. Our approach has ramifications in the domains of mereology, topology, and the theory of location, and the question of the interaction of these three domains within a unified spatial representation theory is addressed. In the final part we also (...) consider the idea of non-standard geographies, which may be associated with geography under a classical conception in the same sense in which non-standard logics are associated with classical logic. (shrink)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common (...) understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development (...) stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Creations of many contemporary artists indicate the emergence of technoculture. Although artistic manifestations of technoculture may appear to be a provocation, they encourage fundamental ontological questions, such as whether a person has unchanging nature; what was and is our relationship to the Other, and what it should be; to what extent can body and mind be altered before they stop being “human”; what is the future of our species. To properly understand the works of technoculture artists, it appears necessary to (...) have a thorough grasp post- and transhumanism as their key sources of inspiration. As a result, the developed tools will be employed to indicate which aspects of technoculture are a manifestation of post- and transhumanist ideas. This analysis is based primarily on the works of Stelarc and Orlan – two widely commented artists of technoculture. (shrink)

This capstone project aimed to develop an offline computer-based assessment (CBA) tool that uses a computer instead of a traditional paper test in evaluating student learning. This addresses the difficulties faced by teachers in administering quarterly assessments. Incorporating technology into student assessment can increase student interest because of the immediate feedback generated automatically and can help teachers improve their work performance. This capstone project employed a developmental approach and utilized a modified ADDIE (Analysis, Design, and Development) model to design (...) the tool using Microsoft PowerPoint and Excel. Ten experts in mathematics, ICT, and assessment validated the face and content validity of the developed CBA tool. Based on the panel’s evaluation, the developed offline CBA tool in Statistics and Probability has passed all the assigned criteria, such as functionality, usability, efficiency, technicality, and accessibility. Overall, the developed CBA tool is suitable for use to address assessment-related issues. (shrink)

In the quest to discover the neural bases of cognition, rigorous behavioral tools are equally as important as sophisticated tools for neural intervention. This paper evaluates several episodes in the development of a novel behavioral tool for rodent cognitive testing, the rodent touchscreen operant chamber. Using conceptual tools on offer in the philosophical literature on exploratory experimentation and control, I illuminate how optimization of this behavioral tool and an understanding of the causal knowledge it may be (...) used to generate historically has involved dynamic interplay between community-driven exploratory practices operating in parallel with causal hypothesis-driven research. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer (...) hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic (...) annotation of large amounts of ncRNA biological and clinical data. (shrink)

Citizens can be meaningfully involved in multiple phases of the urban planning process from decision-making to implementation via a dedicated online platform through which they can interact with planners and decision-makers. In historical contexts, local people are essential resources for decision-makers seeking critical local information needed for effective planning and intervention—including what those citizens recall from the past about the area’s social values and the built environment and what they imagine and hope for their neighborhood’s future. This public knowledge, collected (...) through storytelling and mapping, can play a fundamental role in shaping the framework for neighborhood rehabilitation plans. As a foundation for designing an online visual questionnaire to collect local knowledge and understand the views and expectations of local people, this study focuses on theoretical ideas to define a framework for an online visual questionnaire tool. The tool presented provides a common visual language that people can easily understand and use whatever their social class, education, or background. It also has the benefit of enabling citizens and planners to interact directly regardless of their geographical location. To proposing a framework for the online visual questionnaire, the first step was to review some existing visual tools and methods, including analog used for community engagement and digital used in urban planning to encourage and support public participation. Through an analysis of these methods, some important variables and criteria were identified that further our understanding of citizens’ perceptions of their neighborhoods. The next step, as part of a larger study, will be examining a historical public space, including a bazaar, hammam, and cistern—located in the historical context of Yazd— a central city in Iran registered as a cultural heritage site by UNESCO— as a case study with the larger goal of identifying some specific. (shrink)

Investigating Plato’s ontological as well as epistemological status in each of his dialogues, this book is going to challenge the current theories of Plato’s development and suggest a new one. Regarding the relation of Plato’s early and middle period dialogues, scholars have been divided to two opposing groups: unitarists and developmentalists. While developmentalists try to prove that there are some noticeable and even fundamental differences between Plato’s early and middle period dialogues, the unitarists assert that there is no essential (...) difference in there. The main goal of the first two chapters is to suggest that some of Plato’s ontological as well as epistemological principles change, both radically and fundamentally, between the early and middle period dialogues. Though this is a kind of strengthening the developmentalistic approach corresponding the relation of the early and middle period dialogues, based on the fact that what is to be proved here is a essential development in Plato’ ontology and his epistemology, by expanding the grounds of development to the ontological and epistemological principles, it hints to a more profound development. The fact that the bipolar and split knowledge and being of the early period dialogues give way to the tripartite and bound knowledge and benig of the middle period dialogues indicates the development of the notions of being and knowledge in Plato’s philosophy before the dialogues of the middle period. The first chapter entitled “Plato’s Onto-Epistemological Principles in the Early Dialogues” tries to draw out six principles out of Plato’s early dialogues specially Euthyphro, Laches, Charmides, Hippias Major and Euthydemus. We discuss that these principles present kind of a bipolar as well as split ontology and epistemology. The second chapter, “Revision of First Socrates’ Principles in the Middle Period Dialogues”, aims to argue that the onto-epistemological principles of the early dialogues are being radically changed in three dialogues of Meno, Phaedo and Republic in the middle period dialogues. Not only the bipolar ontology and epistemology of the early dialogues give place to a tripartite ontology and epistemology but also their split being and knowledge are inclined to be replaced by bound being and knowledge. Our next step in this book is to suggest a new approach to Plato’s theory of being in Republic V and Sophist based on the notion of difference and the being of a copy. To understand Plato’s ontology in these two dialogues we are going to suggest a theory we call Pollachos Esti; a name we took from Aristotle’s pollachos legetai both to remind the similarities of the two structures and to reach a consistent view of Plato’s ontology. Based on this theory, when Plato says that something both is and is not, he is applying difference on being which is interpreted here as saying, borrowing Aristotle’s terminology, 'is is (esti) in different senses'. I hope this paper can show how Pollachos Esti can bring forth not only a new approach to Plato’s ontology in Sophist and Republic but also a different approach to being in general. Thence, chapter three, “Pollachos Esti; Plato’s Ontology in Sophist and Republic”, intends to discuss that i) the theories of ‘being as difference’ and ‘being of a copy’, considered together in what we call the theory of pollachos esti, can well be compared to the structure of pollachos legetai in Aristotle when it is attached to the theories of pros hen and substance; and ii) the ontology of Republic V-VII is based on this theory and is, thus, almost the same as the ontology of Sophist. Investigating the most famous chronologies of the last 150 years from Campbell on, the fourth chapter, “The Standard Chronology of the Dialogues”, is to argue that all of them have a somewhat fix and dogmatic arrangement of Plato’s dialogues in which Meno, Phaedo and Republic are located after some early dialogues and before Theaetetus and Parmenides, on the one hand, and all the so-called late period dialogues after Theaetetus and Parmenides on the other hand. It is also reminded that all that the stylometric evidences can show is the lateness and homogeneity of the late period dialogues and, thence, nothing about the relation between dialogues like Theaetetus, Parmenides and Republic. The standard chronology is the subject of many criticisms some of which are discussed in our fifth chapter, “Objections against the Standard Chronology”, in three groups. While the first group of objections criticizes the place of the middle period dialogues immediately after the early ones, the second group attacks the place of late dialogues after the middle ones. The third group includes objections against the place of Parmenides in the standard chronology and tries to show that it cannot be considered after the middle period dialogues. The efforts of the first five chapters lead to a new theory of Plato’s ontological as well as epistemological development in an onto-epistemological chronology of his dialogues in our sixth chapter, “An Onto-Epistemological Chronology of Plato’s dialogues”. Instead of three periods, this chronology includes four waves of dialogues, Socratic wave, ontological wave, epistemological wave and political wave, in which all the so-called middle and late period dialogues are to be interpreted based on the problems presented in Parmenides I. The main changes we suggest in the standard chronology include firstly that Theaetetus and Parmenides I must be posited before Meno and Phaedo and, secondly, Republic must be posited after Sophist. Based on this arrangement, we can find Philosophos, Plato’s promised but unwritten dialogue, inside Republic. (shrink)

Theoretical applications of time and temporality remain a key consideration for both climate scientists and the humanities. By way of extending this importance, we critically examine Timothy Morton’s proposed “ecological awareness” alongside Slavoj Žižek’s “parallax view”. In doing so, the article introduces a “past-present parallax” in order to contest that, while conceptions of the past are marked by “lack”, equally, our conceptions of and relations to Nature remain grounded in an ontological incompleteness, marked by contingency. This novel approach presents an (...) ecological awareness that remains temporally attuned to the impasses and inconsistencies which frame our relations in/with Nature. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. (...) Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

In this dissertation I consider the merits of certain nominalist accounts of phenomena related to the character of ordinary objects. What these accounts have in common is the fact that none of them is an error theory about standard cases of predication and none of them deploys God or uniquely theistic resources in its explanatory framework. -/- The aim of the dissertation is to answer the following questions: -/- • What is the best nominalist account on offer? • How might (...) it be improved? • Does it ultimately succeed? -/- I will argue that while so-called trope theory is the best account on offer, it can be significantly improved—or replaced—by a novel version of nominalism that is modeled after trope theory. Ultimately, however, I will argue that even the novel version fails. -/- The dissertation unfolds as follows. In Chapter 1, I introduce Austere Nominalism (AN), which is perhaps the most extreme version of nominalism that falls within the scope of the dissertation. AN is often described as the view that there exist only concrete particulars. According to AN, it is unnecessary to posit any entities other than ordinary objects—turkeys, tables, and the like—in order to account for explananda related to the character of those objects. (Such explananda include the phenomenon of attribute agreement, of attribute possession, of true subject-predicate sentences, etc.) In this chapter I argue that AN fails to provide an adequate account of these explananda. In addition, introducing and criticizing AN serves an important heuristic role for the rest of the dissertation. To understand this role, we must distinguish between the basic explanatory strategy deployed by the austere nominalist and the type of explananda for which she deploys that strategy. The austere nominalist deploys the strategy to account for the character of ordinary objects. As I argue in Chapter 1, this deployment is a failure. As I go on to show in Chapter 2, the widespread rejection AN has led to a variety of rival accounts of the character of ordinary objects. In rejecting AN, however, these accounts also tacitly reject its basic explanatory strategy. Thus goes the baby with the bathwater, since, arguably, there are some attractive features of AN’s basic explanatory strategy. Indeed, those who defend the most prominent version of nominalism—trope theory—seem to overlook the advantages of AN’s basic strategy, and by so doing, make an unnecessary concession to the realist. Or so I argue in Chapter 3. And, as I will argue in Chapter 4, the strongest version of nominalism is a novel account, modeled after trope theory, that deploys AN’s basic strategy at a more fundamental level than that of ordinary objects. This novel account—troper theory—is closer in spirit to AN than is traditional trope theory. (Thus, AN serves as a foil for the discussion of other nominalist views.) Finally, in the Afterword I indicate how troper theory is equally vulnerable to some of the traditional objections that plague trope theory. Thus, if you are not convinced that traditional objections to trope theory are conclusive and you want to be a nominalist, then you should abandon trope theory and adopt troper theory. If you take traditional objections against trope theory to have significant force, then you should reject both theories. (shrink)

Formal ontology as a main branch of metaphysics investigates categories of being. In the formal ontological approach to metaphysics, these ontological categories are analysed by ontological forms. This analysis, which we illustrate by some category systems, provides a tool to assess the clarity, exactness and intelligibility of different category systems or formal ontologies. We discuss critically different accounts of ontological form in the literature. Of ontological form, we propose a character- neutral relational account. In this metatheory, ontological forms of (...) entities are their standings in internal relations whose holding is neutral on the character of their relata. These relations are “formal ontological relations”. Entities belong to ontological categories because they stand in the same formal ontological relations. We hold a nominalist relationalism about ontological categories and forms. We conclude by showing that our metatheory is useful for understanding categorial fundamentality/non- fundamentality, different formal ontologies, and for unifying metaphysical questions. (shrink)