Barry Smith

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking.

Independently of whether an object of experience becomes a candidate for being a part of the self or a part of the external world, it is always given to us as just an object of experience. The observer-observed relation can be seen as a type of relation with many instances, both between the self and different objects of experience and between any given object of experience and different selves. The self is situated in a spatial grid, where the latter can be characterised as an array of relations, of which the relata include both observers and observed. The world, understood as independent existence, including the self, is empty. However, Paolo Bozzi’s method for identifying the self and delimiting its independent existence from the external world has taught us just the opposite lesson. Bozzi’s project is to teach us how to use them, and to recognise that they allow a self to be situated in a world of objects.

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account.

Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu verstehen. Gleichzeitig werde ich mich bemühen, deutlich zu zeigen, wie eine solch eigenständige Behandlung uns möglicherweise hilft, die Strukturen sowohl der physikalischen Welt als auch der menschlichen Erkenntnis philosophisch besser zu verstehen.

The last decade has witnessed the beginnings of a remarkable convergence of Husserlian phenonenology and analytic philosophy of language, and the present volumes provide original and important texts of the phenomenological philosophy of language. Powerfully influenced by the writings of the early Husserl, Reinach fashioned Husserl’s ideas into a rigorous analytical methodology of his own, which he applied in particular to problems in logic and the theory of knowledge, and to the philosophies of law and psychology. The central role of the concept of state of affairs in Reinach’s philosophy will bring to mind immediately the formal ontology of Wittgenstein’s Tractatus. Reinach’s most significant contribution, however, is contained in his The a priori foundations of civil law (1913), above all in the detailed analysis of the a priori structure of the act of promising. This amounts to an elaborate phenomenological theory of speech acts which anticipates, and in some respects goes beyond, the later theories of Austin and Searle. The present edition is in two volumes. Volume 1, which includes a biographical and thematic introduction by the editors, contains critical editions of those pieces published by Reinach himself. Volume II is a collection of all those items in Reinach’s surviving Nachlass which are in publishable form, including a number of important pieces not hitherto obtainable on such themes as ethical predicates, speech acts (“soziale Akte”), perception and the theory of number, together with a comprehensive sketch of the problems in the theory of knowledge, logic and ethics. Appended to this is a text-critical apparatus which also contains extensive discussions of the origins and sources of the materials in question.

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support.

As is well known, speech acts such as acts of promising can have ontological consequences. For example an act of promising can give rise to a mutually correlated claim and obligation. Increasingly, speech acts in the narrow sense are being augmented by the use of documents of multiple different sorts. In this paper we analyze the results of this augmenta-tion from the ontological point of view, considering especially the domains of law and com-merce. We show how document acts are not isolated phenomena, but rather form large and complex systems with other entities, including occurrent entities such as acts of signing and inspecting, as well as speech acts for example of instructing people to sign or complete a doc-ument. The paper concludes with a consideration of some of the special problems associated with the use of digital documents, for example as concerns issues of security and provenance.

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates.

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.

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists.

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project.

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the body fluids ontology initiative may provide support to basic and translational science.

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies.

We present some ideas on logical process descriptions, using relations from the DIO (Drug Interaction Ontology) as examples and explaining how these relations can be naturally decomposed in terms of more basic structured logical process descriptions using terms from linear logic. In our view, the process descriptions are able to clarify the usual relational descriptions of DIO. In particular, we discuss the use of logical process descriptions in proving linear logical theorems. Among the types of reasoning supported by DIO one can distinguish both (1) basic reasoning about general structures in reality and (2) the domain-specific reasoning of experts. We here propose a clarification of this important distinction between (realist) reasoning on the basis of an ontology and rule-based inferences on the basis of an expert’s view.

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.

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in his "Understanding models understanding language" (2022) for a thesis of this sort. His idea is that (1) where there is semantics there is also understanding and (2) machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics. We show that he goes wrong because he pays insufficient attention to the difference between language as used by humans and the sequences of inert symbols which arise when language is stored on hard drives or in books in libraries.

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters.

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare organizations be combined with models of resources and processes of patient care that are based on a general ontology of social interaction. The Health Level 7 (HL7) is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. HL7 has advanced a widely used messaging standard that enables healthcare applications to exchange clinical and administrative data in digital form. HL7 focuses on the interface requirements of the entire healthcare system and not exclusively on the requirements of one area of healthcare such as pharmacy, medical devices, imaging or insurance transactions. This has inspired the development of a powerful abstract model of patient care called the Reference Information Model (RIM). The present paper begins with an overview of the core classes of the HL7 (Version 3) RIM and a brief discussion of its “actcentered” view of healthcare. Central to this account is what is called the life cycle of events. A clinical action may progress from defined, through planned and ordered, to executed. These modalities of an action are represented as the mood of the act. We then outline the basis of an ontology of organizations, starting from the theory of speech Acts, and apply this ontology to the HL7 RIM. Special attention is given to the sorts of preconditions that must be satisfied for the successful performance of a speech act and to the sorts of entities to which speech acts give rise (e.g. obligations, claims, commitments, etc.). Finally we draw conclusions for the efficient communication and management of medical information and knowledge within and between healthcare organizations, paying special attention to the role that medical documents play in such organizations.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs.

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.

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and formal ontological principles as a first step towards finding answers to this question.

Distinguishes two senses of 'judgment' on the one hand as meaning a state of 'conviction' or 'belief', and on the other hand as meaning an act of 'affirmation' or 'assertion'. Certainly conviction and assertion stand in close relation to each other, but they delineate two heterogeneous logical spheres, and thereby divide the total field of the theory of judgment into two neighbouring but separate sub-fields. Once this is done it is shown to have implications for our understanding especially of the phenomenon of negation, and of the distinction between negation as affirmation of a negative state of affairs, and negation as act of contradicting the judgment someone else has made.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users.

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards.

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some of its anticipated uses.

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population.

I shall begin with the assumption that there are, among our mental acts. some which stand in direct contact with ohjects in the material world. The aim of this paper will he to clarify and to draw out certain implications of this somewhat trivial assumption, and ultimately to say something about the ontological structure of those of our acts which effect the function of bringing us into contact with material acts which serve. as we might say, as the most external points of consciousness which touch the objects consciousness is trying to grasp. Amongst material objects I shall include not only material things such as tables.

Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus on business aspects and not enough on involvement of the right sorts of researchers, in particular those that are able to see how the data and information relate to the entities of concern on the side of the patient. The lack of a central focus on the patient, and the associated focus on ‘concepts’, have spawned a variety of mutually incompatible terminologies exhibiting non-resolvable overlap. The predominance of the healthcare IT industry in the writing and selection of semantic interoperability standards mitigates against the benefits that standards, when well designed, can bring about.