2,566 research outputs found
Coordinating virus research: The Virus Infectious Disease Ontology
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects
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Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
Synonymous relationships among biomedical terms are extensively annotated within specialized terminologies, implying that synonymy is important for practical computational applications within this field. It remains unclear, however, whether text mining actually benefits from documented synonymy and whether existing biomedical thesauri provide adequate coverage of these linguistic relationships. In this study, we examine the impact and extent of undocumented synonymy within a very large compendium of biomedical thesauri. First, we demonstrate that missing synonymy has a significant negative impact on named entity normalization, an important problem within the field of biomedical text mining. To estimate the amount synonymy currently missing from thesauri, we develop a probabilistic model for the construction of synonym terminologies that is capable of handling a wide range of potential biases, and we evaluate its performance using the broader domain of near-synonymy among general English words. Our model predicts that over 90% of these relationships are currently undocumented, a result that we support experimentally through “crowd-sourcing.” Finally, we apply our model to biomedical terminologies and predict that they are missing the vast majority (>90%) of the synonymous relationships they intend to document. Overall, our results expose the dramatic incompleteness of current biomedical thesauri and suggest the need for “next-generation,” high-coverage lexical terminologies.</p
Multidisciplinary perspectives on Artificial Intelligence and the law
This open access book presents an interdisciplinary, multi-authored, edited collection of chapters on Artificial Intelligence (‘AI’) and the Law. AI technology has come to play a central role in the modern data economy. Through a combination of increased computing power, the growing availability of data and the advancement of algorithms, AI has now become an umbrella term for some of the most transformational technological breakthroughs of this age. The importance of AI stems from both the opportunities that it offers and the challenges that it entails. While AI applications hold the promise of economic growth and efficiency gains, they also create significant risks and uncertainty. The potential and perils of AI have thus come to dominate modern discussions of technology and ethics – and although AI was initially allowed to largely develop without guidelines or rules, few would deny that the law is set to play a fundamental role in shaping the future of AI. As the debate over AI is far from over, the need for rigorous analysis has never been greater. This book thus brings together contributors from different fields and backgrounds to explore how the law might provide answers to some of the most pressing questions raised by AI. An outcome of the Católica Research Centre for the Future of Law and its interdisciplinary working group on Law and Artificial Intelligence, it includes contributions by leading scholars in the fields of technology, ethics and the law.info:eu-repo/semantics/publishedVersio
Challenges and perspectives for naming lipids in the context of lipidomics
Introduction: Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. Objectives: In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. Methods & Results: In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. Conclusion: Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks
Explainable Representations for Relation Prediction in Knowledge Graphs
Knowledge graphs represent real-world entities and their relations in a
semantically-rich structure supported by ontologies. Exploring this data with
machine learning methods often relies on knowledge graph embeddings, which
produce latent representations of entities that preserve structural and local
graph neighbourhood properties, but sacrifice explainability. However, in tasks
such as link or relation prediction, understanding which specific features
better explain a relation is crucial to support complex or critical
applications.
We propose SEEK, a novel approach for explainable representations to support
relation prediction in knowledge graphs. It is based on identifying relevant
shared semantic aspects (i.e., subgraphs) between entities and learning
representations for each subgraph, producing a multi-faceted and explainable
representation.
We evaluate SEEK on two real-world highly complex relation prediction tasks:
protein-protein interaction prediction and gene-disease association prediction.
Our extensive analysis using established benchmarks demonstrates that SEEK
achieves significantly better performance than standard learning representation
methods while identifying both sufficient and necessary explanations based on
shared semantic aspects.Comment: 16 pages, 3 figure
Archaeological palaeoenvironmental archives: challenges and potential
This Arts and Humanities Research Council (AHRC) sponsored collaborative doctoral project represents one of
the most significant efforts to collate quantitative and qualitative data that can elucidate practices related to
archaeological palaeoenvironmental archiving in England. The research has revealed that archived
palaeoenvironmental remains are valuable resources for archaeological research and can clarify subjects that
include the adoption and importation of exotic species, plant and insect invasion, human health and diet, and
plant and animal husbandry practices. In addition to scientific research, archived palaeoenvironmental remains
can provide evidence-based narratives of human resilience and climate change and offer evidence of the
scientific process, making them ideal resources for public science engagement. These areas of potential have
been realised at an imperative time; given that waterlogged palaeoenvironmental remains at significant sites
such as Star Carr, Must Farm, and Flag Fen, archaeological deposits in towns and cities are at risk of decay due
to climate change-related factors, and unsustainable agricultural practices. Innovative approaches to collecting
and archiving palaeoenvironmental remains and maintaining existing archives will permit the creation of an
accessible and thorough national resource that can service archaeologists and researchers in the related fields
of biology and natural history. Furthermore, a concerted effort to recognise absences in archaeological
archives, matched by an effort to supply these deficiencies, can produce a resource that can contribute to an
enduring geographical and temporal record of England's biodiversity, which can be used in perpetuity in the
face of diminishing archaeological and contemporary natural resources.
To realise these opportunities, particular challenges must be overcome. The most prominent of these include
inconsistent collection policies resulting from pressures associated with shortages in storage capacity and
declining specialist knowledge in museums and repositories combined with variable curation practices. Many of
these challenges can be resolved by developing a dedicated storage facility that can focus on the ongoing
conservation and curation of palaeoenvironmental remains. Combined with an OASIS + module designed to
handle and disseminate data pertaining to palaeoenvironmental archives, remains would be findable,
accessible, and interoperable with biological archives and collections worldwide. Providing a national centre for
curating palaeoenvironmental remains and a dedicated digital repository will require significant funding.
Funding sources could be identified through collaboration with other disciplines. If sufficient funding cannot be
identified, options that would require less financial investment, such as high-level archive audits and the
production of guidance documents, will be able to assist all stakeholders with the improved curation,
management, and promotion of the archived resource
AI: Limits and Prospects of Artificial Intelligence
The emergence of artificial intelligence has triggered enthusiasm and promise of boundless opportunities as much as uncertainty about its limits. The contributions to this volume explore the limits of AI, describe the necessary conditions for its functionality, reveal its attendant technical and social problems, and present some existing and potential solutions. At the same time, the contributors highlight the societal and attending economic hopes and fears, utopias and dystopias that are associated with the current and future development of artificial intelligence
A Theistic Critique of Secular Moral Nonnaturalism
This dissertation is an exercise in Theistic moral apologetics. It will be developing both a critique of secular nonnaturalist moral theory (moral Platonism) at the level of metaethics, as well as a positive form of the moral argument for the existence of God that follows from this critique. The critique will focus on the work of five prominent metaethical theorists of secular moral non-naturalism: David Enoch, Eric Wielenberg, Russ Shafer-Landau, Michael Huemer, and Christopher Kulp. Each of these thinkers will be critically examined. Following this critique, the positive moral argument for the existence of God will be developed, combining a cumulative, abductive argument that follows from filling in the content of a succinct apagogic argument. The cumulative abductive argument and the apagogic argument together, with a transcendental and modal component, will be presented to make the case that Theism is the best explanation for the kind of moral, rational beings we are and the kind of universe in which we live, a rational intelligible universe
Predicate Matrix: an interoperable lexical knowledge base for predicates
183 p.La Matriz de Predicados (Predicate Matrix en inglés) es un nuevo recurso léxico-semántico resultado de la integración de múltiples fuentes de conocimiento, entre las cuales se encuentran FrameNet, VerbNet, PropBank y WordNet. La Matriz de Predicados proporciona un léxico extenso y robusto que permite mejorar la interoperabilidad entre los recursos semánticos mencionados anteriormente. La creación de la Matriz de Predicados se basa en la integración de Semlink y nuevos mappings obtenidos utilizando métodos automáticos que enlazan el conocimiento semántico a nivel léxico y de roles. Asimismo, hemos ampliado la Predicate Matrix para cubrir los predicados nominales (inglés, español) y predicados en otros idiomas (castellano, catalán y vasco). Como resultado, la Matriz de predicados proporciona un léxico multilingüe que permite el análisis semántico interoperable en múltiples idiomas
Terminology and ontology development for semantic annotation : A use case on sepsis and adverse events
publishedVersio
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