Databases

This paper responds to the question of whether the Internet has made lectures obsolete and Matthew Pickles’ investigation of why lectures persist. It is written as a pastiche of R.K. Narayan, about whom a somewhat parallel question is probably asked. Pickles refers to a logic lecturer so dry people went swimming, and a pastiche approach is an alternative.

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Wearable devices are increasingly present in the health context, as tools for biomedical research and clinical care. In this context, wearables are considered key tools for a more digital, personalised, preventive medicine. At the same time, wearables have also been associated with issues and risks, such as those connected to privacy and data sharing. Yet, discussions in the literature have mostly focused on either technical or ethical considerations, framing these as largely separate areas of discussion, and the contribution of wearables (...) to the collection, development, application of biomedical knowledge has only partially been discussed. To fill in these gaps, in this article we provide an epistemic (knowledgerelated) overview of the main functions of wearable technology for health: monitoring, screening, detection, and prediction. On this basis, we identify 4 areas of concern in the application of wearables for these functions: data quality, balanced estimations, health equity, and fairness. To move the field forward in an effective and beneficial direction, we present recommendations for the 4 areas: local standards of quality, interoperability, access, and representativity. (shrink)

Ever since the era of internet had ushered in cloud computing, there had been increase in the demand for the unlimited data available through cloud computing for data analysis, pattern recognition and technology advancement. With this also bring the problem of scalability, efficiency and security threat. This research paper focuses on how data can be dynamically mine in real time for pattern detection in a secure cloud computing environment using combination of decision tree algorithm and Random Forest over a restful (...) Application Programming Interface (API). We are able to successfully Implement data mining on cloud computing bypassing or avoiding direct interaction with data warehouse and without any terminal involve by using combination of IBM Cloud storage facility, Amazing Web Service, Application Programming Interface and Window service along with a decision tree and Random Forest algorithm for our classifier. We were able to successfully bypass direct connection with the data warehouse and cloud terminal with 94% accuracy in our model. (shrink)

FDE is a logic that captures relevant entailment between implication-free formulae and admits of an intuitive informational interpretation as a 4-valued logic in which “a computer should think”. However, the logic is co-NP complete, and so an idealized model of how an agent can think. We address this issue by shifting to signed formulae where the signs express imprecise values associated with two distinct bipartitions of the set of standard 4 values. Thus, we present a proof system which consists of (...) linear operational rules and only two branching structural rules, the latter expressing a generalized rule of bivalence. This system naturally leads to defining an infinite hierarchy of tractable depth-bounded approximations to FDE. Namely, approximations in which the number of nested applications of the two branching rules is bounded. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

While scientific inquiry crucially relies on the extraction of patterns from data, we still have a far from perfect understanding of the metaphysics of patterns—and, in particular, of what makes a pattern real. In this paper we derive a criterion of real-patternhood from the notion of conditional Kolmogorov complexity. The resulting account belongs to the philosophical tradition, initiated by Dennett :27–51, 1991), that links real-patternhood to data compressibility, but is simpler and formally more perspicuous than other proposals previously defended in (...) the literature. It also successfully enforces a non-redundancy principle, suggested by Ladyman and Ross, that aims to exclude from real-patternhood those patterns that can be ignored without loss of information about the target dataset, and which their own account fails to enforce. (shrink)

In this commentary, I propose a framework for thinking about data quality in the context of scientific research. I start by analyzing conceptualizations of quality as a property of information, evidence and data and reviewing research in the philosophy of information, the philosophy of science and the philosophy of biomedicine. I identify a push for purpose dependency as one of the main results of this review. On this basis, I present a contextual approach to data quality in scientific research, whereby (...) the quality of a dataset is dependent on the context of use of the dataset as much as the dataset itself. I exemplify the approach by discussing current critiques and debates of scientific quality, thus showcasing how data quality can be approached contextually. (shrink)

In this paper we investigate if sentences presented as the result of the application of statistical models and artificial intelligence to large volumes of data – the so-called ‘Big Data’ – can be characterized as semantically true, or as quasi-true, or even if such sentences can only be characterized as probably quasi-false and, in a certain way, post-true; that is, if, in the context of Big Data, the representation of a data domain can be configured as a total structure, or (...) as a partial structure provided with a set of sentences assumed to be true, or if such representation cannot be configured as a partial structure provided with a set of sentences assumed to be true. (shrink)

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? (shrink)

Starting from texts and data collected during the installation of the online database DArIL (Digital Archive of Inaugural Lectures at Renaissance and Early Modern Universities), the paper presents some results of this work. It is divided in two sections: in the first one, Marco Forlivesi describes DArIL, its structure, content, aims, and potential. In the second part, Iolanda Ventura attempts to distinguish the various types of lectiones inaugurales by focusing on specific texts dealing with medicine produced at the Universities of (...) Padua, Jena, and Helmstedt during the Eighteenth Century. -/- . (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...) and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

The orbital space environment is home to natural and artificial satellites, debris, and space weather phenomena. As the population of orbital objects grows so do the potential hazards to astronauts, space infrastructure and spaceflight capability. Orbital debris, in particular, is a universal concern. This and other hazards can be minimized by improving global space situational awareness (SSA). By sharing more data and increasing observational coverage of the space environment we stand to achieve that goal, thereby making spaceflight safer and expanding (...) our knowledge of near-Earth space. To facilitate data-sharing interoperability among distinct orbital debris and space object catalogs, and SSA information systems, I proposed ontology in (Rovetto, 2015) and (Rovetto and Kelso, 2016). I continue this effort toward formal representations and models of the overall domain that may serve to improve peaceful SSA and increase our scientific knowledge. This paper explains the project concept introduced in those publications, summarizing efforts to date as well as the research field of ontology development and engineering. I describe concepts for an ontological framework for the orbital space environment, near-Earth space environment and SSA domain. An ontological framework is conceived as a part of a potential international information system. The purpose of such a system is to consolidate, analyze and reason over various sources and types of orbital and SSA data toward the mutually beneficial goals of safer space navigation and scientific research. Recent internationals findings on the limitations of orbital data, in addition to existing publications on collaborative SSA, demonstrate both the overlap with this project and the need for data-sharing and integration. (shrink)

Space situational awareness (SSA) is vital for international safety and security, and for the future of space travel. The sharing of SSA data and information should improve the state of global SSA for planetary defense and spaceflight safety. I take steps toward a Space Situational Awareness (SSA) Ontology, and outline some central objectives, requirements and desiderata in the ontology development process for this domain. The purpose of this ontological system is to explore the potential for the ontology research topic to (...) (i) represent SSA general knowledge, data, and entities/objects, (ii) clearly express the meaning of SSA data, and (iii) foster SSA data-sharing. The overall goal and motivation is to (iv) improve our capacity for planetary defense, e.g., from near- or deep-space objects and phenomena, and (v) facilitate safer and peaceful space access, navigation and travel, by improving global SSA. This research is thereby intended only for peaceful space-domain applications and uses, with particular interests in orbital debris. There is little application of ontology to the space domain as compared with other disciplines and little if any ontological development of SSA and related domains. In this respect, this paper offers novel concepts. (shrink)

We introduce here evoText, a new tool for automated analysis of the literature in the biological sciences. evoText contains a database of hundreds of thousands of journal articles and an array of analysis tools for generating quantitative data on the nature and history of life science, especially ecology and evolutionary biology. This article describes the features of evoText, presents a variety of examples of the kinds of analyses that evoText can run, and offers a brief tutorial describing how to use (...) it. (shrink)

This paper develops the ontology of space objects for theoretical and computational ontology applied to the space (astronautical/astronomical) domain. It follows “An ontological architecture for Orbital Debris Data” (Rovetto, 2015) and “Preliminaries of a Space Situational Awareness Ontology” (Rovetto, Kelso, 2016). Important considerations for developing a space object ontology, or more broadly, a space domain ontology are presented. The main category term ‘Space Object’ is analyzed from a philosophical perspective. The ontological commitments of legal definitions for artificial space objects are (...) also discussed. Space object taxonomies are offered and space object terms are defined. (shrink)

A short summary paper of my Orbital Space Domain Ontology project (purl.org/space-ontology), originally conceived in 2011. Since then I've sought (without success) opportunities to realize it (either as a PhD or other degree thesis; or in an employment position) toward my original passion of entering the space sector and gaining further space education. Since then persons in the relevant space disciplines have seen the potential in it, and unfortunately some have taken advantage of my ideas yet excluded me from work. (...) I continue to struggle to fight for my own ideas as I see others professionally and financially benefit at my expense. References and documentation are available upon request to confirm my early ideation and origination on this topic. Please contact me if you have opportunities. Thank you. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA domain (...) knowledge, (II) structure, and standardize where needed, orbital data and terminology, and (III) foster semantic interoperability and data-sharing. In doing so I hope to (IV) contribute to solving the orbital debris problem, improving peaceful global SSA, and ensuring safe space travel for future generations. (shrink)

The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.

As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...) benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future. (shrink)

Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.

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)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (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)

Two large lexicological projects for the Center for the Greek Language, Thessaloniki, were to be published in print and on the WWW, which meant that two conversions were needed: a near-database file had to be converted to fully formatted file for printing and a fully formatted file had to be converted to a database for WWW access. As it turned out, both conversions could make use of existing clues that indicated the kinds of information contained in each particular piece of (...) text, thus separating fields from each other and ordering them into a tree-like structure. This indicates that both forms of the dictionaries, print and database, stem from the same cognitive need to categorize information into a kind of information before further understanding – be this for a human reader or for a machine. (shrink)