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)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions (...) such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions. (shrink)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...) approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We (...) examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...) fact necessary for understanding and using terminologies and ontologies in science. -/- This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose. (shrink)

We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) is about. (shrink)

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

David Hume’s thought has interrupted entire disciplines from dogmatic slumbers. Yet Hume’s influence is even more expansive and continuous than we might have thought. There are two significant areas of inquiry where Hume’s influence has not been adequately appreciated or articulated: analytic phenomenology and analytic process philosophy. My dissertation explores these traditions’ indebtedness to Hume by engaging with the work of Edmund Husserl and Alfred North Whitehead, who introduce consequential changes into their systems in direct response to what they see (...) as Humean problems with their initial models. Three major themes are of special interest. First, vis-à-vis “Unity of Mind,” each philosopher asks what accounts for the apparent unity of mind and experience, including what principles connect distinct experiences. Second, vis-à-vis “Temporal Awareness,” each philosopher inquires into what grounds temporality and the experience of temporal passage, including what principles connect distinct moments. Third, vis-à-vis “Personal Identity,” each philosopher investigates what constitutes the experience of continuity and unity over time, including personal continuity and unity qua “personal identity.” A fourth concordance is methodological. In pursuing the aforementioned themes, each philosopher accords epistemic primacy to lived experience and what discloses itself therein. An overarching Humean problem for all, correlatively, is how continuity and unity arise from distinct items: perceptions, intentional experiences, and actual occasions, respectively. My dissertation attempts to explicate this and related systematic issues from a historical perspective informed by contemporary analytic metaphysics, philosophy of mind, and recent scholarship in Hume, Husserl, and Whitehead studies. Chapter One argues that Hume’s infamous “Appendix problem” concerns reconciling the incontrovertible unity of mind with his unrenounceable epistemological principle that the mind never perceives real connections between distinct perceptions. Chapter Two traces Hume’s proto-phenomenological influence on Husserl’s theories (not theory) of temporal awareness. Chapter Three examines Hume’s proto-processual influence on Whitehead's theories (not theory) of personal identity. Unfortunately, neither Husserl nor Whitehead read each other’s work. Nevertheless, both take Hume to be the one who knocks at, yet ultimately fails to walk through the doors that his explorations unveil. By so doing, they beg that we do the same with them. (shrink)

Here, I lay the foundations of a high-level ontology of particulars whose structuring principles differ radically from the 'continuant' vs. 'occurrent' distinction traditionally adopted in applied ontology. These principles are derived from a new analysis of the ontology of “occurring” or “happening” entities. Firstly, my analysis integrates recent work on the ontology of processes, which brings them closer to objects in their mode of existence and persistence by assimilating them to continuant particulars. Secondly, my analysis distinguishes clearly between processes and (...) events, in order to make the latter abstract objects of thought (alongside propositions). Lastly, I open my ontological inventory to properties and facts, the existence of which is commonly admitted. By giving specific roles to these primitives, the framework allows one to account for static and dynamic aspects of the physical world and for the way that subjects conceive its history: facts account for the life of substances (physical objects and processes), whereas events enable cognitive subjects to account for the life story of substances. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

Despre analogia existentă între aspectele epistemologice şi metodologice ale activităţii serviciilor de informaţii şi unele discipline ştiinţifice, pledând pentru o abordare mai ştiinţifică a procesului de culegere şi analiză de informaţii din cadrul ciclului de informaţii. Afirm că în prezent aspectele teoretice, ontologice şi epistemologice, în activitatea multor servicii de informaţii, sunt subestimate, determinând înţelegere incompletă a fenomenelor actuale şi creând confuzie în colaborarea inter-instituţională. După o scurtă Introducere, care include o istorie a evoluţiei conceptului de serviciu de informaţii după (...) al doilea război mondial, în Activitatea de informaţii definesc obiectivele şi organizarea serviciilor de informaţii, modelul de bază al acestor organizaţii (ciclul informaţional), şi aspectele relevante ale culegerii de informaţii şi analizei de informaţii. În secţiunea Ontologia evidenţiez aspectele ontologice şi entităţile care ameninţă şi sunt ameninţate. Secţiunea Epistemologie include aspecte specifice activităţii de informaţii, cu analiza principalului model (Singer) folosit în mod tradiţional, şi expun o posibilă abordare epistemologică prin prisma conceptului de cunoaştere tacită dezvoltat de omul de ştiinţă Michael Polanyi. În secţiunea Metodologii prezint diverse teorii metodologice cu accent pe tehnicile analitice structurale, şi câteva analogii, cu ştiinţa, arheologia, afacerile şi medicina. Lucrarea se încheie cu Concluziile privind posibilitatea unei abordări mai ştiinţifice a metodelor de culegere şi analiză a informaţiilor din cadrul serviciilor de informaţii. -/- Cuvinte cheie: servicii de informaţii, agenţii de informaţii, informaţii, intelligence -/- CUPRINS -/- Abstract 1. Introducere 1.1. Istorie 2. Activitatea de informaţii 2.1. Organizaţii 2.2. Ciclul informaţional 2.3. Colectarea informaţiilor 2.4. Analiza informaţiilor 2.5. Contrainformatii 2.6. Comunităţi epistemice 3. Ontologia 4. Epistemologia 4.1. Cunoaşterea tacită (Polanyi) 5. Metodologii 6. Analogii cu alte discipline 6.1. Stiinta 6.2. Arheologia 6.3. Afaceri 6.4. Medicina 7. Concluzii Bibliografie -/- ISBN: 978-606-033-160-5 , DOI: 10.58679/TW56764. (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)

Grenon and Smith (2004) propose a framework for the ontology of things in space and time involving and invoking the distinction between continuants and occurrents, which has become a key element of Basic Formal Ontology (BFO). The terminology of SNAP (from “snapshot:” state of a continuant at a time) and SPAN (how an occurrent develops over an interval or timespan) occurs in that paper’s title. While any commonsense ontology will have a place for both continuants and occurrents, there is much (...) room for philosophical debate on whether one of them is more basic than the other, or can be reduced to the other, or whether they are equally fundamental, or whether they are two different perspectives on the same reality. Grenon and Smith opt for the last of these. They call the accounts of continuants (SNAP) and occurrents (SPAN) both “ontologies.” They do not have a single ontology of all that is in space and time. This dialog throws a few of the common arguments around a bit and comes to no sure conclusion. But one of the characters bears a faint resemblance to a certain Buffalonian philosopher. (shrink)

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.

A survey of the similarities and differences between BFO and DOLCE, and of the mutual interactions between Nicola Guarino and Barry Smith.

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

What follows is a contribution to the horizontal integration of warfighter intelligence data as defined in Chairman of the Joint Chiefs of Staff Instruction J2 CJCSI 3340.02AL: -/- Horizontally integrating warfighter intelligence data improves the consumers’ production, analysis and dissemination capabilities. HI requires access (including discovery, search, retrieval, and display) to intelligence data among the warfighters and other producers and consumers via standardized services and architectures. These consumers include, but are not limited to, the combatant commands, Services, Defense agencies, and (...) the Intelligence Community. (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...) status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

The Ontological Square is a categorial scheme that combines two metaphysical distinctions: that between types (or universals ) and tokens (or particulars ) on the one hand, and that between characters (or features ) and their substrates (or bearers ) on the other hand. The resulting four-fold classification of things comprises particular substrates, called substances , universal substrates, called kinds , particular characters, called modes or moments , and universal characters, called attributes . Things are joined together in facts by (...) primitive ontological ties or nexus . This article describes a logic that is meant to capture the basic intuitions behind the Ontological Square. Given a minimal correspondence between atomic logical form and ontological structure, the commitment to nexus as a distinct ontological category entails a rehabilitation of copulae as ties of predication. Thus, the Logic of the Ontological Square is a copula calculus rather than a predicate calculus; its soundness and completeness can be established with respect to a model akin to a so-called first-order semantics for standard second-order logic. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The General Formal Ontology (GFO) is a top-level ontology that is being developed at the University of Leipzig since 1999. Besides introducing some of the basic principles of the ontology, we expound axiomatic fragments of its formalization and present ontological models of several use cases. GFO is a top-level ontology that integrates objects and processes into a unified framework, in a way that differs significantly from other ontologies. Another unique selling feature of GFO is its meta-ontological architecture, which includes set (...) theory into ontology and which accounts for its specific role in common representation approaches. The second level of that architecture starts from the distinction of categories and individuals, which forms the backbone of the world’s structure. Furthermore, GFO comprises several kinds of categories, among them universals and concepts, and it considers several ontological regions and levels. In the context of this special issue paper, we study five pre-determined use cases from the perspective of GFO. The results of these analyses yield insights into how the ontology treats several important notions. Very abridged, this covers material objects and their composition; roles and social entities; properties with their relations to objects and processes, and their changing; changes of processes, including a functional perspective; and, eventually, the nature and changing of concepts as well as terminology. A final part summarizes application projects that use GFO in various contexts. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies (...) via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)