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1.
Eur Heart J ; 44(9): 713-725, 2023 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-36629285

RESUMEN

Artificial intelligence (AI) is increasingly being utilized in healthcare. This article provides clinicians and researchers with a step-wise foundation for high-value AI that can be applied to a variety of different data modalities. The aim is to improve the transparency and application of AI methods, with the potential to benefit patients in routine cardiovascular care. Following a clear research hypothesis, an AI-based workflow begins with data selection and pre-processing prior to analysis, with the type of data (structured, semi-structured, or unstructured) determining what type of pre-processing steps and machine-learning algorithms are required. Algorithmic and data validation should be performed to ensure the robustness of the chosen methodology, followed by an objective evaluation of performance. Seven case studies are provided to highlight the wide variety of data modalities and clinical questions that can benefit from modern AI techniques, with a focus on applying them to cardiovascular disease management. Despite the growing use of AI, further education for healthcare workers, researchers, and the public are needed to aid understanding of how AI works and to close the existing gap in knowledge. In addition, issues regarding data access, sharing, and security must be addressed to ensure full engagement by patients and the public. The application of AI within healthcare provides an opportunity for clinicians to deliver a more personalized approach to medical care by accounting for confounders, interactions, and the rising prevalence of multi-morbidity.


Asunto(s)
Inteligencia Artificial , Sistema Cardiovascular , Humanos , Algoritmos , Aprendizaje Automático , Atención a la Salud
2.
Lancet ; 398(10309): 1427-1435, 2021 10 16.
Artículo en Inglés | MEDLINE | ID: mdl-34474011

RESUMEN

BACKGROUND: Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of ß-blocker efficacy in patients with sinus rhythm and atrial fibrillation. METHODS: Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of ß blockers. All-cause mortality during median 1·3 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012). FINDINGS: 15 659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12 822), most clusters demonstrated a consistent overall mortality benefit from ß blockers, with odds ratios (ORs) ranging from 0·54 to 0·74. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0·86, 95% CI 0·67-1·10; p=0·22). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of ß blockers versus placebo (OR 0·92, 0·77-1·10; p=0·37). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with ß blockers (OR 0·57, 0·35-0·93; p=0·023). The robustness and consistency of clustering was confirmed for all models (p<0·0001 vs random), and cluster membership was externally validated across the nine independent trials. INTERPRETATION: An artificial intelligence-based clustering approach was able to distinguish prognostic response from ß blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where ß blockers did reduce mortality. FUNDING: Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.


Asunto(s)
Antagonistas Adrenérgicos beta/uso terapéutico , Fibrilación Atrial/tratamiento farmacológico , Análisis por Conglomerados , Insuficiencia Cardíaca/tratamiento farmacológico , Aprendizaje Automático , Anciano , Comorbilidad , Método Doble Ciego , Femenino , Insuficiencia Cardíaca/mortalidad , Humanos , Masculino , Persona de Mediana Edad , Volumen Sistólico , Función Ventricular Izquierda
3.
BMC Med Inform Decis Mak ; 22(1): 33, 2022 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-35123470

RESUMEN

BACKGROUND: Semantic similarity is a valuable tool for analysis in biomedicine. When applied to phenotype profiles derived from clinical text, they have the capacity to enable and enhance 'patient-like me' analyses, automated coding, differential diagnosis, and outcome prediction. While a large body of work exists exploring the use of semantic similarity for multiple tasks, including protein interaction prediction, and rare disease differential diagnosis, there is less work exploring comparison of patient phenotype profiles for clinical tasks. Moreover, there are no experimental explorations of optimal parameters or better methods in the area. METHODS: We develop a platform for reproducible benchmarking and comparison of experimental conditions for patient phentoype similarity. Using the platform, we evaluate the task of ranking shared primary diagnosis from uncurated phenotype profiles derived from all text narrative associated with admissions in the medical information mart for intensive care (MIMIC-III). RESULTS: 300 semantic similarity configurations were evaluated, as well as one embedding-based approach. On average, measures that did not make use of an external information content measure performed slightly better, however the best-performing configurations when measured by area under receiver operating characteristic curve and Top Ten Accuracy used term-specificity and annotation-frequency measures. CONCLUSION: We identified and interpreted the performance of a large number of semantic similarity configurations for the task of classifying diagnosis from text-derived phenotype profiles in one setting. We also provided a basis for further research on other settings and related tasks in the area.


Asunto(s)
Enfermedades Raras , Semántica , Humanos , Fenotipo , Curva ROC
4.
BMC Med ; 19(1): 23, 2021 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-33472631

RESUMEN

BACKGROUND: The National Early Warning Score (NEWS2) is currently recommended in the UK for the risk stratification of COVID-19 patients, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for the prediction of severe COVID-19 outcome and identify and validate a set of blood and physiological parameters routinely collected at hospital admission to improve upon the use of NEWS2 alone for medium-term risk stratification. METHODS: Training cohorts comprised 1276 patients admitted to King's College Hospital National Health Service (NHS) Foundation Trust with COVID-19 disease from 1 March to 30 April 2020. External validation cohorts included 6237 patients from five UK NHS Trusts (Guy's and St Thomas' Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals, University Hospitals Birmingham), one hospital in Norway (Oslo University Hospital), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID-19 disease (transfer to intensive care unit (ICU) or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity, and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models. RESULTS: A baseline model of 'NEWS2 + age' had poor-to-moderate discrimination for severe COVID-19 infection at 14 days (area under receiver operating characteristic curve (AUC) in training cohort = 0.700, 95% confidence interval (CI) 0.680, 0.722; Brier score = 0.192, 95% CI 0.186, 0.197). A supplemented model adding eight routinely collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, C-reactive protein, estimated glomerular filtration rate, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI 0.715, 0.757), and these improvements were replicated across seven UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites. CONCLUSIONS: NEWS2 score had poor-to-moderate discrimination for medium-term COVID-19 outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID.


Asunto(s)
COVID-19/diagnóstico , Puntuación de Alerta Temprana , Anciano , COVID-19/epidemiología , COVID-19/virología , Estudios de Cohortes , Registros Electrónicos de Salud , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pandemias , Pronóstico , SARS-CoV-2/aislamiento & purificación , Medicina Estatal , Reino Unido/epidemiología
5.
BMC Med Inform Decis Mak ; 20(Suppl 10): 311, 2020 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-33319712

RESUMEN

BACKGROUND: Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions. METHODS: We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combined sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. In addition, we designed and implemented a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying a small set of axioms that, when removed, result in a consistent and coherent set of ontologies. RESULTS: We tested the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes. We also applied our semi-automatic repair algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes, finding that only 117 axioms could be removed to account for all cases of unsatisfiability across all OBO ontologies. CONCLUSIONS: We identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.


Asunto(s)
Ontologías Biológicas , Semántica , Algoritmos , Humanos
6.
BMC Bioinformatics ; 16: 26, 2015 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-25627673

RESUMEN

BACKGROUND: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. RESULTS: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net . CONCLUSIONS: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.


Asunto(s)
Proteínas Reguladoras de la Apoptosis/análisis , Ontologías Biológicas , Biología Computacional/métodos , Defectos del Tabique Interventricular/genética , Modelos Genéticos , Programas Informáticos , Bases de Datos Factuales , Estudio de Asociación del Genoma Completo , Humanos , Internet , Conocimiento , Lenguaje , Fenotipo , Semántica
7.
Artículo en Inglés | MEDLINE | ID: mdl-39435971

RESUMEN

AIM: Psychosis is associated with significant health and societal costs. Early intervention in psychosis services (EIP) are highly effective in promoting recovery, yet substantial proportions of young people disengage. The current study aimed to develop and evaluate a novel engagement intervention in EIP services. METHOD: A qualitative investigation of facilitators and barriers to engagement in 68 first episode psychosis patients, family members and young people, and a Delphi consultation with 27 regional and national youth and psychosis service leads informed the development of the intervention. A mixed-methods feasibility-pilot study then compared engagement outcomes in 298 EIP service users in two cohorts: standard EIP versus standard EIP plus the novel early youth-engagement (EYE) intervention. A qualitative study explored intervention experiences in 22 randomly selected service users, carers and clinicians. A process evaluation explored delivery. RESULTS: Disengagement was 24% in the standard EIP cohort compared to 14.5% in the standard EIP plus EYE intervention cohort. A 95% Bayesian credibility interval revealed a 95% probability that the true reduction in disengagement lay somewhere between 0% and 18%. The number needed to treat was 11, 95% CI [5, 242]. Use of the EYE resources was associated with engagement. Qualitiative feedback supported effects on communication, social network engagement, service user goals, mental health and well-being outcomes. CONCLUSION: The EYE intervention was designed from a service user, young person and carer perspective. Both qualitative and quantitative data support impacts on engagement. We now need to evaluate effectiveness, cost-effectiveness and implementation in a multi-site randomised controlled trial.

8.
Sci Rep ; 13(1): 14660, 2023 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-37669983

RESUMEN

Link prediction in complex networks has recently attracted a great deal of attraction in diverse scientific domains, including social and biological sciences. Given a snapshot of a network, the goal is to predict links that are missing in the network or that are likely to occur in the near future. This problem has both theoretical and practical significance; it not only helps us to identify missing links in a network more efficiently by avoiding the expensive and time consuming experimental processes, but also allows us to study the evolution of a network with time. To address the problem of link prediction, numerous attempts have been made over the recent years that exploit the local and the global topological properties of the network to predict missing links in the network. In this paper, we use parametrised matrix forest index (PMFI) to predict missing links in a network. We show that, for small parameter values, this index is linked to a heat diffusion process on a graph and therefore encodes geometric properties of the network. We then develop a framework that combines the PMFI with a local similarity index to predict missing links in the network. The framework is applied to numerous networks obtained from diverse domains such as social network, biological network, and transport network. The results show that the proposed method can predict missing links with higher accuracy when compared to other state-of-the-art link prediction methods.

9.
Int J Radiat Biol ; 99(8): 1291-1300, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36735963

RESUMEN

The era of high-throughput techniques created big data in the medical field and research disciplines. Machine intelligence (MI) approaches can overcome critical limitations on how those large-scale data sets are processed, analyzed, and interpreted. The 67th Annual Meeting of the Radiation Research Society featured a symposium on MI approaches to highlight recent advancements in the radiation sciences and their clinical applications. This article summarizes three of those presentations regarding recent developments for metadata processing and ontological formalization, data mining for radiation outcomes in pediatric oncology, and imaging in lung cancer.


Asunto(s)
Inteligencia Artificial , Neoplasias Pulmonares , Niño , Humanos , Macrodatos , Minería de Datos
10.
Contemp Clin Trials ; 120: 106882, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35973663

RESUMEN

BACKGROUND: Real-world evidence (RWE) plays an increasingly important role within global regulatory and reimbursement processes. RWE generation can be enhanced by collecting and using patient-reported outcomes (PROs), which can provide valuable information on the effectiveness, safety, and tolerability of health interventions from the patient perspective. This analysis aims to examine and summarise the utilisation of patient-reported outcomes measures (PROMs) in real-world studies. METHODS: Descriptions of phase IV trials were downloaded on July 22, 2021 from the Clinicaltrials.gov database since its inception. An automated algorithm was built to detect trials utilising PROMs and composite measures including patient-reported components. Search terms were developed based on the PROQOLID database. RESULTS: Of 27,976 phase IV clinical trials posted on Clinicaltrials.gov between 1999 and July 2021, 21% and 4% used PROMs and composite measures, respectively. Recent years demonstrated a steady increase in the utilisation of PROMs in phase IV trials. CONCLUSIONS: The use of PROMs in phase IV trials seems to be lower than its use in earlier phases of clinical research. Increased uptake of PROMs in RWE studies can be facilitated in a number of ways including the development of standards for their collection, analysis and use.


Asunto(s)
Ensayos Clínicos Fase IV como Asunto , Medición de Resultados Informados por el Paciente , Humanos
11.
NPJ Digit Med ; 5(1): 186, 2022 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-36544046

RESUMEN

Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union's funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019-2022 was 80 times that of 2007-2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP's great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models.

12.
Front Digit Health ; 3: 781227, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34939069

RESUMEN

Semantic similarity is a useful approach for comparing patient phenotypes, and holds the potential of an effective method for exploiting text-derived phenotypes for differential diagnosis, text and document classification, and outcome prediction. While approaches for context disambiguation are commonly used in text mining applications, forming a standard component of information extraction pipelines, their effects on semantic similarity calculations have not been widely explored. In this work, we evaluate how inclusion and disclusion of negated and uncertain mentions of concepts from text-derived phenotypes affects similarity of patients, and the use of those profiles to predict diagnosis. We report on the effectiveness of these approaches and report a very small, yet significant, improvement in performance when classifying primary diagnosis over MIMIC-III patient visits.

13.
J Biomed Semantics ; 12(1): 7, 2021 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-33845909

RESUMEN

BACKGROUND: Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described by several concepts in the same or similar contexts across several ontologies. While these concepts describe the same entities, they contain different sets of complementary metadata. Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks. RESULTS: We develop and present an algorithm that expands the set of labels associated with an ontology class using a combination of strict lexical matching and cross-ontology reasoner-enabled equivalency queries. Across all disease terms in the Disease Ontology, the approach found 51,362 additional labels, more than tripling the number defined by the ontology itself. Manual validation by a clinical expert on a random sampling of expanded synonyms over the Human Phenotype Ontology yielded a precision of 0.912. Furthermore, we found that annotating patient visits in MIMIC-III with an extended set of Disease Ontology labels led to semantic similarity score derived from those labels being a significantly better predictor of matching first diagnosis, with a mean average precision of 0.88 for the unexpanded set of annotations, and 0.913 for the expanded set. CONCLUSIONS: Inter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. While the accuracy of the extended vocabulary is not perfect, it nevertheless led to a significantly improved ontology-based characterisation of patients from text in one setting. Furthermore, where run-on error is not acceptable, the technique can be used to provide candidate synonyms which can be checked by a domain expert.


Asunto(s)
Ontologías Biológicas , Vocabulario , Minería de Datos , Ecosistema , Humanos , Vocabulario Controlado
14.
Comput Biol Med ; 130: 104216, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33484944

RESUMEN

Negation detection is an important task in biomedical text mining. Particularly in clinical settings, it is of critical importance to determine whether findings mentioned in text are present or absent. Rule-based negation detection algorithms are a common approach to the task, and more recent investigations have resulted in the development of rule-based systems utilising the rich grammatical information afforded by typed dependency graphs. However, interacting with these complex representations inevitably necessitates complex rules, which are time-consuming to develop and do not generalise well. We hypothesise that a heuristic approach to determining negation via dependency graphs could offer a powerful alternative. We describe and implement an algorithm for negation detection based on grammatical distance from a negatory construct in a typed dependency graph. To evaluate the algorithm, we develop two testing corpora comprised of sentences of clinical text extracted from the MIMIC-III database and documents related to hypertrophic cardiomyopathy patients routinely collected at University Hospitals Birmingham NHS trust. Gold-standard validation datasets were built by a combination of human annotation and examination of algorithm error. Finally, we compare the performance of our approach with four other rule-based algorithms on both gold-standard corpora. The presented algorithm exhibits the best performance by f-measure over the MIMIC-III dataset, and a similar performance to the syntactic negation detection systems over the HCM dataset. It is also the fastest of the dependency-based negation systems explored in this study. Our results show that while a single heuristic approach to dependency-based negation detection is ignorant to certain advanced cases, it nevertheless forms a powerful and stable method, requiring minimal training and adaptation between datasets. As such, it could present a drop-in replacement or augmentation for many-rule negation approaches in clinical text-mining pipelines, particularly for cases where adaptation and rule development is not required or possible.


Asunto(s)
Algoritmos , Heurística , Minería de Datos , Bases de Datos Factuales , Humanos , Lenguaje , Procesamiento de Lenguaje Natural
15.
Comput Biol Med ; 133: 104360, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33836447

RESUMEN

Ontology-based phenotype profiles have been utilised for the purpose of differential diagnosis of rare genetic diseases, and for decision support in specific disease domains. Particularly, semantic similarity facilitates diagnostic hypothesis generation through comparison with disease phenotype profiles. However, the approach has not been applied for differential diagnosis of common diseases, or generalised clinical diagnostics from uncurated text-derived phenotypes. In this work, we describe the development of an approach for deriving patient phenotype profiles from clinical narrative text, and apply this to text associated with MIMIC-III patient visits. We then explore the use of semantic similarity with those text-derived phenotypes to classify primary patient diagnosis, comparing the use of patient-patient similarity and patient-disease similarity using phenotype-disease profiles previously mined from literature. We also consider a combined approach, in which literature-derived phenotypes are extended with the content of text-derived phenotypes we mined from 500 patients. The results reveal a powerful approach, showing that in one setting, uncurated text phenotypes can be used for differential diagnosis of common diseases, making use of information both inside and outside the setting. While the methods themselves should be explored for further optimisation, they could be applied to a variety of clinical tasks, such as differential diagnosis, cohort discovery, document and text classification, and outcome prediction.


Asunto(s)
Enfermedades Raras , Semántica , Diagnóstico Diferencial , Humanos , Fenotipo , Enfermedades Raras/diagnóstico , Enfermedades Raras/genética
16.
Comput Biol Med ; 138: 104904, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34600327

RESUMEN

Identification of ontology concepts in clinical narrative text enables the creation of phenotype profiles that can be associated with clinical entities, such as patients or drugs. Constructing patient phenotype profiles using formal ontologies enables their analysis via semantic similarity, in turn enabling the use of background knowledge in clustering or classification analyses. However, traditional semantic similarity approaches collapse complex relationships between patient phenotypes into a unitary similarity scores for each pair of patients. Moreover, single scores may be based only on matching terms with the greatest information content (IC), ignoring other dimensions of patient similarity. This process necessarily leads to a loss of information in the resulting representation of patient similarity, and is especially apparent when using very large text-derived and highly multi-morbid phenotype profiles. Moreover, it renders finding a biological explanation for similarity very difficult; the black box problem. In this article, we explore the generation of multiple semantic similarity scores for patients based on different facets of their phenotypic manifestation, which we define through different sub-graphs in the Human Phenotype Ontology. We further present a new methodology for deriving sets of qualitative class descriptions for groups of entities described by ontology terms. Leveraging this strategy to obtain meaningful explanations for our semantic clusters alongside other evaluation techniques, we show that semantic clustering with ontology-derived facets enables the representation, and thus identification of, clinically relevant phenotype relationships not easily recoverable using overall clustering alone. In this way, we demonstrate the potential of faceted semantic clustering for gaining a deeper and more nuanced understanding of text-derived patient phenotypes.


Asunto(s)
Semántica , Análisis por Conglomerados , Humanos , Fenotipo
17.
Comput Biol Med ; 135: 104542, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34139439

RESUMEN

BACKGROUND: Unstructured text created by patients represents a rich, but relatively inaccessible resource for advancing patient-centred care. This study aimed to develop an ontology for ocular immune-mediated inflammatory diseases (OcIMIDo), as a tool to facilitate data extraction and analysis, illustrating its application to online patient support forum data. METHODS: We developed OcIMIDo using clinical guidelines, domain expertise, and cross-references to classes from other biomedical ontologies. We developed an approach to add patient-preferred synonyms text-mined from oliviasvision.org online forum, using statistical ranking. We validated the approach with split-sampling and comparison to manual extraction. Using OcIMIDo, we then explored the frequency of OcIMIDo classes and synonyms, and their potential association with natural language sentiment expressed in each online forum post. FINDINGS: OcIMIDo (version 1.2) includes 661 classes, describing anatomy, clinical phenotype, disease activity status, complications, investigations, interventions and functional impacts. It contains 1661 relationships and axioms, 2851 annotations, including 1131 database cross-references, and 187 patient-preferred synonyms. To illustrate OcIMIDo's potential applications, we explored 9031 forum posts, revealing frequent mention of different clinical phenotypes, treatments, and complications. Language sentiment analysis of each post was generally positive (median 0.12, IQR 0.01-0.24). In multivariable logistic regression, the odds of a post expressing negative sentiment were significantly associated with first posts as compared to replies (OR 3.3, 95% CI 2.8 to 3.9, p < 0.001). CONCLUSION: We report the development and validation of a new ontology for inflammatory eye diseases, which includes patient-preferred synonyms, and can be used to explore unstructured patient or physician-reported text data, with many potential applications.


Asunto(s)
Ontologías Biológicas , Bases de Datos Factuales , Humanos , Lenguaje , Fenotipo
18.
Nanomaterials (Basel) ; 10(12)2020 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-33322568

RESUMEN

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a "nano" extension to the InChI standard.

19.
J Am Soc Echocardiogr ; 32(12): 1505-1515, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31653530

RESUMEN

Echocardiography plays an essential role in the diagnosis and assessment of cardiovascular disease. Measurements derived from echocardiography are also used to determine the severity of disease, its progression over time, and to aid in the choice of optimal therapy. It is therefore clinically important that echocardiographic measurements be reproducible, repeatable, and reliable. There are a variety of statistical tests available to assess these parameters, and in this article the authors summarize those available for use by echocardiographers to improve their clinical practice. Correlation coefficients, linear regression, Bland-Altman plots, and the coefficient of variation are explored, along with their limitations. The authors also provide an online tool for the easy calculation of these statistics in the clinical environment (www.birmingham.ac.uk/echo). Quantifying and enhancing the reproducibility of echocardiography has important potential to improve the value of echocardiography as the basis for good clinical decision-making.


Asunto(s)
Enfermedades Cardiovasculares/diagnóstico por imagen , Ecocardiografía/métodos , Guías de Práctica Clínica como Asunto , Enfermedades Cardiovasculares/epidemiología , Femenino , Humanos , Modelos Lineales , Masculino , Reproducibilidad de los Resultados , Reino Unido
20.
Front Psychol ; 7: 424, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27065907

RESUMEN

The experience of hearing distressing voices has recently attracted much attention in the literature on psychological therapies. A new "wave" of therapies is considering voice hearing experiences within a relational framework. However, such therapies may have limited impact if they do not precisely target key psychological variables within the voice hearing experience and/or ensure there is a "fit" between the profile of the hearer and the therapy (the so-called "What works for whom" debate). Gender is one aspect of both the voice and the hearer (and the interaction between the two) that may be influential when selecting an appropriate therapy, and is an issue that has thus far received little attention within the literature. The existing literature suggests that some differences in voice hearing experience are evident between the genders. Furthermore, studies exploring interpersonal relating in men and women more generally suggest differences within intimate relationships in terms of distancing and emotionality. The current study utilized data from four published studies to explore the extent to which these gender differences in social relating may extend to relating within the voice hearing experience. The findings suggest a role for gender as a variable that can be considered when identifying an appropriate psychological therapy for a given hearer.

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