706 research outputs found

    The Human Phenotype Ontology in 2024: phenotypes around the world.

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    The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

    The Human Phenotype Ontology in 2024: phenotypes around the world

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    \ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

    Design of new algorithms for gene network reconstruction applied to in silico modeling of biomedical data

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    Programa de Doctorado en Biotecnología, Ingeniería y Tecnología QuímicaLínea de Investigación: Ingeniería, Ciencia de Datos y BioinformáticaClave Programa: DBICódigo Línea: 111The root causes of disease are still poorly understood. The success of current therapies is limited because persistent diseases are frequently treated based on their symptoms rather than the underlying cause of the disease. Therefore, biomedical research is experiencing a technology-driven shift to data-driven holistic approaches to better characterize the molecular mechanisms causing disease. Using omics data as an input, emerging disciplines like network biology attempt to model the relationships between biomolecules. To this effect, gene co- expression networks arise as a promising tool for deciphering the relationships between genes in large transcriptomic datasets. However, because of their low specificity and high false positive rate, they demonstrate a limited capacity to retrieve the disrupted mechanisms that lead to disease onset, progression, and maintenance. Within the context of statistical modeling, we dove deeper into the reconstruction of gene co-expression networks with the specific goal of discovering disease-specific features directly from expression data. Using ensemble techniques, which combine the results of various metrics, we were able to more precisely capture biologically significant relationships between genes. We were able to find de novo potential disease-specific features with the help of prior biological knowledge and the development of new network inference techniques. Through our different approaches, we analyzed large gene sets across multiple samples and used gene expression as a surrogate marker for the inherent biological processes, reconstructing robust gene co-expression networks that are simple to explore. By mining disease-specific gene co-expression networks we come up with a useful framework for identifying new omics-phenotype associations from conditional expression datasets.In this sense, understanding diseases from the perspective of biological network perturbations will improve personalized medicine, impacting rational biomarker discovery, patient stratification and drug design, and ultimately leading to more targeted therapies.Universidad Pablo de Olavide de Sevilla. Departamento de Deporte e Informátic

    Modern meat: the next generation of meat from cells

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    Modern Meat is the first textbook on cultivated meat, with contributions from over 100 experts within the cultivated meat community. The Sections of Modern Meat comprise 5 broad categories of cultivated meat: Context, Impact, Science, Society, and World. The 19 chapters of Modern Meat, spread across these 5 sections, provide detailed entries on cultivated meat. They extensively tour a range of topics including the impact of cultivated meat on humans and animals, the bioprocess of cultivated meat production, how cultivated meat may become a food option in Space and on Mars, and how cultivated meat may impact the economy, culture, and tradition of Asia

    Ontology-driven and weakly supervised rare disease identification from clinical notes

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    BACKGROUND: Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. METHODS: We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. RESULTS: The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). CONCLUSION: The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies

    Development and application of a platform for harmonisation and integration of metabolomics data

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    Integrating diverse metabolomics data for molecular epidemiology analyses provides both opportuni- ties and challenges in the field of human health research. Combining patient cohorts may improve power and sensitivity of analyses but is challenging due to significant technical and analytical vari- ability. Additionally, current systems for the storage and analysis of metabolomics data suffer from scalability, query-ability, and integration issues that limit their adoption for molecular epidemiological research. Here, a novel platform for integrative metabolomics is developed, which addresses issues of storage, harmonisation, querying, scaling, and analysis of large-scale metabolomics data. Its use is demonstrated through an investigation of molecular trends of ageing in an integrated four-cohort dataset where the advantages and disadvantages of combining balanced and unbalanced cohorts are explored, and robust metabolite trends are successfully identified and shown to be concordant with previous studies.Open Acces

    NEGOTIATING THE SACRED: UNDERSTANDING IMPACTS TO IKS AND ITEK FROM USE OF REMOTE SENSING AND GIS TECHNOLOGIES WITHIN TRIBAL LANDSCAPES

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    How we see the world and ourselves in relation to it is largely achieved by the lens we are looking through and associated experiences within this relationship. This is additionally true when considering the acknowledged fact that Indigenous Knowledges are derived from natural and cultural sources and these assist in constituting the cultural identities of those Peoples associated with these sources. Presently there is a hunger for access and use of Indigenous Knowledges (IK) as never before seen in public ways, through a national Call for collaborative means to apply these knowledges to such as the issues we globally face as a result of Climate Change. What are Indigenous Knowledges? How are they created? Who holds these and can utilize them in public ways? These questions are an embedded aspect of this Call that requires attention. Further, what impacts exist that benefit, but also challenge, the endeavor to utilize Indigenous Knowledges outside local areas where they are derived? What of these sacred ways of knowing are being negotiated to attain their use? Five areas of concern were identified in response to these questions through application of An Indigenous Research Way (AIRW), a novel continuous improvement model for implementing Indigenous Research Methodologies and Methods, within research design and practice. Synthesizing these concerns into three themes, Education, Technology, and Tribal Leader Decision-Making, awareness was revealed of these as first level and gateway impacts. Indigenous ways of knowing, being, and doing operationalizes Indigenous worldviews about relationality and this as central to how Indigenous Knowledges Systems (IKS) are created and in turn create Indigenous Traditional Ecological Knowledges (ITEK). Understanding how we “see” ourselves in relation to this process is imperative. A burgeoning method for seeing landscapes, and they as sources of IK, is through use of remote sensing and Geographical Information Systems (GIS). This Phase I study, through a Kin-based Case Study and mixed-methods approach, sought to understand impacts to IKS and ITEK from use of these technologies within tribal landscapes through review and assessment of 73 ESRI tribal GIS public StoryMap projects, led by tribal practitioners, accomplished in 2017 - 2021. Assessment provides there exists an assumption that identifying as being Indigenous includes being a holder of cultural knowledges and that these are utilized at will and regularly. The data troubles this assumption with respect to tribal individuals trained as practitioners of these technologies and their use of ITEK then provided through public digital media. Impacts to IKS and ITEK reveal enhancements and also replacement of the “seeing” accomplished by Indigenous People through technological means and the public perceptions of their cultural lifeways and persona of being Holders of Indigenous Knowledges. These impacts are broad in their implications as they attend to not only understandings of past and present access to ITEK but also future applications that brings the conversation into the realms of understanding being Indigenous off-earth

    Managing healthcare transformation towards P5 medicine (Published in Frontiers in Medicine)

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    Health and social care systems around the world are facing radical organizational, methodological and technological paradigm changes to meet the requirements for improving quality and safety of care as well as efficiency and efficacy of care processes. In this they’re trying to manage the challenges of ongoing demographic changes towards aging, multi-diseased societies, development of human resources, a health and social services consumerism, medical and biomedical progress, and exploding costs for health-related R&D as well as health services delivery. Furthermore, they intend to achieve sustainability of global health systems by transforming them towards intelligent, adaptive and proactive systems focusing on health and wellness with optimized quality and safety outcomes. The outcome is a transformed health and wellness ecosystem combining the approaches of translational medicine, 5P medicine (personalized, preventive, predictive, participative precision medicine) and digital health towards ubiquitous personalized health services realized independent of time and location. It considers individual health status, conditions, genetic and genomic dispositions in personal social, occupational, environmental and behavioural context, thus turning health and social care from reactive to proactive. This requires the advancement communication and cooperation among the business actors from different domains (disciplines) with different methodologies, terminologies/ontologies, education, skills and experiences from data level (data sharing) to concept/knowledge level (knowledge sharing). The challenge here is the understanding and the formal as well as consistent representation of the world of sciences and practices, i.e. of multidisciplinary and dynamic systems in variable context, for enabling mapping between the different disciplines, methodologies, perspectives, intentions, languages, etc. Based on a framework for dynamically, use-case-specifically and context aware representing multi-domain ecosystems including their development process, systems, models and artefacts can be consistently represented, harmonized and integrated. The response to that problem is the formal representation of health and social care ecosystems through an system-oriented, architecture-centric, ontology-based and policy-driven model and framework, addressing all domains and development process views contributing to the system and context in question. Accordingly, this Research Topic would like to address this change towards 5P medicine. Specifically, areas of interest include, but are not limited: • A multidisciplinary approach to the transformation of health and social systems • Success factors for sustainable P5 ecosystems • AI and robotics in transformed health ecosystems • Transformed health ecosystems challenges for security, privacy and trust • Modelling digital health systems • Ethical challenges of personalized digital health • Knowledge representation and management of transformed health ecosystems Table of Contents: 04 Editorial: Managing healthcare transformation towards P5 medicine Bernd Blobel and Dipak Kalra 06 Transformation of Health and Social Care Systems—An Interdisciplinary Approach Toward a Foundational Architecture Bernd Blobel, Frank Oemig, Pekka Ruotsalainen and Diego M. Lopez 26 Transformed Health Ecosystems—Challenges for Security, Privacy, and Trust Pekka Ruotsalainen and Bernd Blobel 36 Success Factors for Scaling Up the Adoption of Digital Therapeutics Towards the Realization of P5 Medicine Alexandra Prodan, Lucas Deimel, Johannes Ahlqvist, Strahil Birov, Rainer Thiel, Meeri Toivanen, Zoi Kolitsi and Dipak Kalra 49 EU-Funded Telemedicine Projects – Assessment of, and Lessons Learned From, in the Light of the SARS-CoV-2 Pandemic Laura Paleari, Virginia Malini, Gabriella Paoli, Stefano Scillieri, Claudia Bighin, Bernd Blobel and Mauro Giacomini 60 A Review of Artificial Intelligence and Robotics in Transformed Health Ecosystems Kerstin Denecke and Claude R. Baudoin 73 Modeling digital health systems to foster interoperability Frank Oemig and Bernd Blobel 89 Challenges and solutions for transforming health ecosystems in low- and middle-income countries through artificial intelligence Diego M. López, Carolina Rico-Olarte, Bernd Blobel and Carol Hullin 111 Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems Markus Kreuzthaler, Mathias Brochhausen, Cilia Zayas, Bernd Blobel and Stefan Schulz 126 The ethical challenges of personalized digital health Els Maeckelberghe, Kinga Zdunek, Sara Marceglia, Bobbie Farsides and Michael Rigb
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