Biomedical ontologies: What part-of is and isn’t

AbstractMereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this practice leaves some basic issues unanswered: type constraints of mereological relations, e.g., concerning artifacts and biological entities, the relation between parthood and time, inferred parts and wholes as well as a delimitation of parthood against spatial inclusion. Furthermore, mereological relations can be asserted not only between physical objects but also between biological processes and medical procedures. We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies

Medical knowledge reengineering – converting major portions of the UMLS into a terminological knowledge base

Abstract We describe a semi-automatic knowledge engineering approach for converting the human anatomy and pathology portion of the UMLS metathesaurus into a terminological knowledge base. Particular attention is paid to the proper representation of part-whole hierarchies, which complement taxonomic ones as a major hierarchy-forming principle for anatomical knowledge. Our approach consists of four steps. First, concept definitions are automatically generated from the metathesaurus, with LOOM as the target language. Second, integrity checking of the emerging taxonomic and partonomic hierarchies is automatically carried out by the terminological classifier. Third, terminological cycles and inconsistencies are manually eliminated and, in the last step, the knowledge base built this way is incrementally refined by a medical expert. Our experiments were run on a terminological knowledge base which is composed of 164 000 concepts and 76 000 relations. Empirical evidence for the lack of logical consistency, adequacy and improper granularity of the UMLS knowledge source is given, and finally, assessments of what kind of efforts are needed to render the formal target representation structures complete and empirically adequate

Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain

This paper investigates implicit knowledge in two ontologies of anatomy: the Foundational Model of Anatomy and GALEN. The methods consist of extracting the knowledge explicitly represented, acquiring the implicit knowledge through augmentation and inference techniques, and identifying the origin of each semantic relation. The number of relations (12 million in FMA and 4.6 million in GALEN), broken down by source, is presented. Major findings include: each technique provides specific relations; and many relations can be generated by more than one technique. The application of these findings to ontology auditing, validation, and maintenance is discussed, as well as the application to ontology integratio

Relationality and health: developing a transversal neurotheological account of the pathways linking social connection, immune function, and health outcomes

This thesis is a transdisciplinary investigation of the link between social connection and health outcomes. Its twofold aim is to explore the nature of this relationship and build a theoretical model for a possible causal chain between the two, and to develop and deploy a new model for engaging the very different discourses of theology and neuroscience. To this end it draws on both theological reflection and on experimental scientific data from cognitive neuroscience and psychoneuroimmunology. The opening half of the work establishes the wider epistemological and methodological frameworks within which the project is set, and also the specific framework for the particular area of study. The first of these involves a critical analysis of the tensions at the heart of the dialogue between science and religion, and of the specific difficulties faced by the emerging sub-discipline of neurotheology. It then dissects and further develops the interdisciplinary dialogical model devised by J Wentzel van Huyssteen, in order to enable it to generate and support additional transdisciplinary outputs. In the second of the two framework arenas, the concept of health itself is first explored, and then epidemiological, Biblical, and immunological accounts of the link between relational connection and health are examined in order to establish that sufficient common ground exists to warrant a neurotheological approach to investigating the question of how the two are connected. The second half of the thesis then uses the developed model as a basis for engaging theological and neuroscientific perspectives on human relationality. This takes the form of three transversal encounters, each centred around a specific aspect of this: relationality as basic, as emergent, and as realised. From the output of these three dialogical interactions, a neurotheologically framed argument is developed to support the contention that relationality is an emergent phenomenon of a complex system concerned with social monitoring and response, and thus the way in which it is realised can exert causal constraints on system components. Finally a theoretical model is derived from this argument for a pathway linking relational experience to health outcomes via alterations in allostatic maintenance mechanisms

Kind Historicism & Biological Ontology

This thesis develops a new theory of natural kinds for the biological world, called ‘Kind Historicism’, and addresses the relationship between natural kind theorizing and scientific reasoning. Applied to natural kinds and individuals in biology, Kind Historicism provides an ontology of the biological world. Discussions of biological ontology have struggled to balance insights from scientific practice with tools from analytic philosophy, metaphysics, and ontology. Ontological questions and practical/epistemic questions are often entangled. This thesis separates the two enquires, explaining why an ontological account of ‘what-there-is’ in biology should not straightforwardly dictate scientific categories, objects, or concepts. More precisely this thesis provides, in two parts, the development of Kind Historicism in light of discussions of natural kinds, essentialism, and monism, followed by the application of Kind Historicism to the natural kind status of biochemicals and to the problem of biological individuality. Finally, the success of Kind Historicism is measured against its ability to account for ‘intrinsic heterogeneity’ and ‘theoretical pluralism’, features of the biological world and science, respectively, believed to preclude biological natural kinds

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

(b2023 to 2014) The UNBELIEVABLE similarities between the ideas of some people (2006-2016) and my ideas (2002-2008) in physics (quantum mechanics, cosmology), cognitive neuroscience, philosophy of mind, and philosophy (this manuscript would require a REVOLUTION in international academy environment!)

(b2023 to 2014) The UNBELIEVABLE similarities between the ideas of some people (2006-2016) and my ideas (2002-2008) in physics (quantum mechanics, cosmology), cognitive neuroscience, philosophy of mind, and philosophy (this manuscript would require a REVOLUTION in international academy environment!

Predictive embodied concepts: an exploration of higher cognition within the predictive processing paradigm

Predictive processing, an increasingly popular paradigm in cognitive sciences, has focused primarily on giving accounts of perception, motor control and a host of psychological phenomena, including consciousness. But higher cognitive processes, like conceptual thought, language, and logic, have received only limited attention to date and PP still stands disconnected from a huge body of research in those areas. In this thesis, I aim to address this gap and I attempt to go some way towards developing and defending a cognitive-computational approach to higher cognition within the predictive processing paradigm. To test its explanatory potential, I apply it to a range of linguistic and conceptual phenomena. I proceed in three steps. First, I lay out an account of concepts and suggest how concepts are represented, how they can be context-sensitively processed, and how the apparent diversity of formats arise. Secondly, I propose how paradigmatic higher cognitive competencies, like language and logical reasoning, could fit into the PP picture. Thirdly, I apply the PP account of concepts and language to a range of linguistic-conceptual phenomena as test cases, namely: metaphor, the semantic paradox (specifically the Liar Paradox) and copredication. Finally, I discuss some challenges and objections to the PP framework as applied to higher cognition and in general

Gabriel Vacariu (c2023 to 2014) The UNBELIEVABLE similarities between the ideas of some people (2006-2016) and my ideas (2002-2008) in physics (quantum mechanics, cosmology), cognitive neuroscience, philosophy of mind, and philosophy

Unbelievable similar ideas to my ideas published long before..