Clinical Bioinformatics: challenges and opportunities

Background: Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods: In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results: Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of –omics information. Conclusions: Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput “-omics” technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research

Clinical Bioinformatics: Challenges and Opportunities

Background: Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results: Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information. Conclusions: Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research

Evaluating the informatics for integrating biology and the bedside system for clinical research

pre-printBackground: Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort selection tool from the Informatics for Integrating Biology and the Bedside (i2b2) group: the i2b2 hive. Methods: Our evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone. Results: We found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre-or post-processing, modifications to the hive metadata, etc. Conclusion: The i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be transformed to fit the logical data models of the i2b2 hive, strategies for extracting relevant clinical data from source systems, and the ability to perform substantial pre- and post-processing of these data

ASSESSMENT OF RISK SCORES FOR THE PREDICTION AND DETECTION OF TYPE 2 DIABETES MELLITUS IN CLINICAL SETTINGS

Health and sociological indicators confirm that life expectancy is increasing, and so, the years that patients have to live with chronic diseases and co-morbidities. Type 2 Diabetes is one of the most common chronic diseases, specially linked to overweight and ages over sixty. As a metabolic disease, Type 2 Diabetes affects multiple organs by causing damage in blood vessels and nervous system at micro and macro scale. Mortality of subjects with diabetes is three times higher than the mortality for subjects with other chronic diseases. On the one hand, the management of diabetes is focused on the maintenance of the blood glucose levels under a threshold by the prescription of anti-diabetic drugs and a combination of healthy food habits and moderate physical activity. Recent studies have demonstrated the effectiveness of new strategies to delay and even prevent the onset of Type 2 Diabetes by a combination of active and healthy lifestyle on cohorts of mid to high risk subjects. On the other hand, prospective research has been driven on large groups of population to build risk scores which aim to obtain a rule for the classification of patients according to the odds for developing the disease. Currently there are more than two hundred models and risk scores for doing this, but a few have been properly evaluated in external groups and, to date, none of them has been tested on a population based study. The research study presented in this doctoral thesis strives to use externally validated risk scores for the prediction and detection of Type 2 Diabetes on a population data base in Hospital La Fe (Valencia, Spain). The study hypothesis is that the integration of existing prediction and detection risk scores on Electronic Health Records increases the early-detection of high risk cases. To evaluate this hypothesis three studies on the clinical, user and technology dimensions have been driven to evaluate the extent to which the models and the hospital is ready to exploit such models to identify high risk groups and drive efficient preventive strategies. The findings presented in this thesis suggest that Electronic Health Records are not prepared to massively feed risk models. Some of the evaluated models have shown a good classification performance, which accompanied to the well-acceptance of web-based tools and the acceptable technical performance of the information and communication technology system, suggests that after some work these models can effectively drive a new paradigm of active screening for Type 2 Diabetes.Los indicadores de salud y sociológicos confirman que la esperanza de vida está aumentando, y por lo tanto, los años que los pacientes tienen que vivir con enfermedades crónicas y comorbilidades. Diabetes tipo 2 es una de las enfermedades crónicas más comunes, especialmente relacionadas con el sobrepeso y edades superiores a los sesenta años. Como enfermedad metabólica, la diabetes tipo 2 afecta a múltiples órganos causando daño en los vasos sanguíneos y el sistema nervioso a escala micro y macro. La mortalidad de sujetos con diabetes es tres veces mayor que la mortalidad de sujetos con otras enfermedades crónicas. Por un lado, la estrategia de manejo se centra en el mantenimiento de los niveles de glucosa en sangre bajo un umbral mediante la prescripción de fármacos antidiabéticos y una combinación de hábitos alimentarios saludables y actividad física moderada. Estudios recientes han demostrado la eficacia de nuevas estrategias para retrasar e incluso prevenir la aparición de la diabetes tipo 2 mediante una combinación de estilo de vida activo y saludable en cohortes de sujetos de riesgo medio a alto. Por otro lado, la investigación prospectiva se ha dirigido a grupos de la población para construir modelos de riesgo que pretenden obtener una regla para la clasificación de las personas según las probabilidades de desarrollar la enfermedad. Actualmente hay más de doscientos modelos de riesgo para hacer esta identificación, no obstante la inmensa mayoría no han sido debidamente evaluados en grupos externos y, hasta la fecha, ninguno de ellos ha sido probado en un estudio poblacional. El estudio de investigación presentado en esta tesis doctoral pretende utilizar modelos riesgo validados externamente para la predicción y detección de la Diabetes Tipo 2 en una base de datos poblacional del Hospital La Fe de Valencia (España). La hipótesis del estudio es que la integración de los modelos de riesgo de predicción y detección existentes la práctica clínica aumenta la detección temprana de casos de alto riesgo. Para evaluar esta hipótesis, se han realizado tres estudios sobre las dimensiones clínicas, del usuario y de la tecnología para evaluar hasta qué punto los modelos y el hospital están dispuestos a explotar dichos modelos para identificar grupos de alto riesgo y conducir estrategias preventivas eficaces. Los hallazgos presentados en esta tesis sugieren que los registros de salud electrónicos no están preparados para alimentar masivamente modelos de riesgo. Algunos de los modelos evaluados han demostrado un buen desempeño de clasificación, lo que acompañó a la buena aceptación de herramientas basadas en la web y el desempeño técnico aceptable del sistema de tecnología de información y comunicación, sugiere que después de algún trabajo estos modelos pueden conducir un nuevo paradigma de la detección activa de la Diabetes Tipo 2.Els indicadors sociològics i de salut confirmen un augment en l'esperança de vida, i per tant, dels anys que les persones han de viure amb malalties cròniques i comorbiditats. la diabetis de tipus 2 és una de les malalties cròniques més comunes, especialment relacionades amb l'excés de pes i edats superiors als seixanta anys. Com a malaltia metabòlica, la diabetis de tipus 2 afecta múltiples òrgans causant dany als vasos sanguinis i el sistema nerviós a escala micro i macro. La mortalitat de subjectes amb diabetis és tres vegades superior a la mortalitat de subjectes amb altres malalties cròniques. D'una banda, l'estratègia de maneig se centra en el manteniment dels nivells de glucosa en sang sota un llindar mitjançant la prescripció de fàrmacs antidiabètics i una combinació d'hàbits alimentaris saludables i activitat física moderada. Estudis recents han demostrat l'eficàcia de noves estratègies per a retardar i fins i tot prevenir l'aparició de la diabetis de tipus 2 mitjançant una combinació d'estil de vida actiu i saludable en cohorts de subjectes de risc mitjà a alt. D'altra banda, la investigació prospectiva s'ha dirigit a grups específics de la població per construir models de risc que pretenen obtenir una regla per a la classificació de les persones segons les probabilitats de desenvolupar la malaltia. Actualment hi ha més de dos-cents models de risc per fer aquesta identificació, però la immensa majoria no han estat degudament avaluats en grups externs i, fins ara, cap d'ells ha estat provat en un estudi poblacional. L'estudi d'investigació presentat en aquesta tesi doctoral utilitza models de risc validats externament per a la predicció i detecció de diabetis de tipus 2 en una base de dades poblacional de l'Hospital La Fe de València (Espanya). La hipòtesi de l'estudi és que la integració dels models de risc de predicció i detecció existents la pràctica clínica augmenta la detecció de casos d'alt risc. Per avaluar aquesta hipòtesi, s'han realitzat tres estudis sobre les dimensions clíniques, de l'usuari i de la tecnologia per avaluar fins a quin punt els models i l'hospital estan disposats a explotar aquests models per identificar grups d'alt risc i conduir estratègies preventives. Les troballes presentades sugereixen que els registres de salut electrònics no estan preparats per alimentar massivament models de risc. Alguns dels models avaluats han demostrat una bona classificació, el que va acompanyar a la bona acceptació d'eines basades en el web i el rendiment tècnic acceptable del sistema de tecnologia d'informació i comunicacions implementat. La conclusió es que encara es necesari treball per que aquests models poden conduir un nou paradigma de la detecció activa de la diabetis de tipus 2.Martínez Millana, A. (2017). ASSESSMENT OF RISK SCORES FOR THE PREDICTION AND DETECTION OF TYPE 2 DIABETES MELLITUS IN CLINICAL SETTINGS [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86209TESI

Evaluating the informatics for integrating biology and the bedside system for clinical research

<p>Abstract</p> <p>Background</p> <p>Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort selection tool from the Informatics for Integrating Biology and the Bedside (i2b2) group: the i2b2 hive.</p> <p>Methods</p> <p>Our evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone.</p> <p>Results</p> <p>We found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre- or post-processing, modifications to the hive metadata, etc.</p> <p>Conclusion</p> <p>The i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be transformed to fit the logical data models of the i2b2 hive, strategies for extracting relevant clinical data from source systems, and the ability to perform substantial pre- and post-processing of these data.</p

Integration of Distributed Services and Hybrid Models Based on Process Choreography to Predict and Detect Type 2 Diabetes

[EN] Life expectancy is increasing and, so, the years that patients have to live with chronic diseases and co-morbidities. Type 2 diabetes is one of the most prevalent chronic diseases, specifically linked to being overweight and ages over sixty. Recent studies have demonstrated the effectiveness of new strategies to delay and even prevent the onset of type 2 diabetes by a combination of active and healthy lifestyle on cohorts of mid to high risk subjects. Prospective research has been driven on large groups of the population to build risk scores that aim to obtain a rule for the classification of patients according to the odds for developing the disease. Currently, there are more than two hundred models and risk scores for doing this, but a few have been properly evaluated in external groups and integrated into a clinical application for decision support. In this paper, we present a novel system architecture based on service choreography and hybrid modeling, which enables a distributed integration of clinical databases, statistical and mathematical engines and web interfaces to be deployed in a clinical setting. The system was assessed during an eight-week continuous period with eight endocrinologists of a hospital who evaluated up to 8080 patients with seven different type 2 diabetes risk models implemented in two mathematical engines. Throughput was assessed as a matter of technical key performance indicators, confirming the reliability and efficiency of the proposed architecture to integrate hybrid artificial intelligence tools into daily clinical routine to identify high risk subjects.The authors wish to acknowledge the consortium of the MOSAIC project (funded by the European Commission, Grant No. FP7-ICT 600914) for their commitment during concept development, which led to the development of the research reported in this manuscriptMartinez-Millana, A.; Bayo-Monton, JL.; Argente-Pla, M.; Fernández Llatas, C.; Merino-Torres, JF.; Traver Salcedo, V. (2018). Integration of Distributed Services and Hybrid Models Based on Process Choreography to Predict and Detect Type 2 Diabetes. Sensors. 18 (1)(79):1-26. https://doi.org/10.3390/s18010079S12618 (1)79Thomas, C. C., & Philipson, L. H. (2015). Update on Diabetes Classification. Medical Clinics of North America, 99(1), 1-16. doi:10.1016/j.mcna.2014.08.015Kahn, S. 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Identification of Relationships Between Patients Through Elements in a Data Warehouse Using the Familial, Associational, and Incidental Relationship (FAIR) Initiative: A Pilot Study

BACKGROUND: Over the last several years there has been widespread development of medical data warehouses. Current data warehouses focus on individual cases, but lack the ability to identify family members that could be used for dyadic or familial research. Currently, the patient\u27s family history in the medical record is the only documentation we have to understand the health status and social habits of their family members. Identifying familial linkages in a phenotypic data warehouse can be valuable in cohort identification and in beginning to understand the interactions of diseases among families. OBJECTIVE: The goal of the Familial, Associational, and Incidental Relationships (FAIR) initiative is to identify an index set of patients\u27 relationships through elements in a data warehouse. METHODS: Using a test set of 500 children, we measured the sensitivity and specificity of available linkage algorithm identifiers (eg, insurance identification numbers and phone numbers) and validated this tool/algorithm through a manual chart audit. RESULTS: Of all the children, 52.4% (262/500) were male, and the mean age of the cohort was 8 years old (SD 5). Of the children, 51.6% (258/500) were identified as white in race. The identifiers used for FAIR were available for the majority of patients: insurance number (483/500, 96.6%), phone number (500/500, 100%), and address (497/500, 99.4%). When utilizing the FAIR tool and various combinations of identifiers, sensitivity ranged from 15.5% (62/401) to 83.8% (336/401), and specificity from 72% (71/99) to 100% (99/99). The preferred method was matching patients using insurance or phone number, which had a sensitivity of 72.1% (289/401) and a specificity of 94% (93/99). Using the Informatics for Integrating Biology and the Bedside (i2b2) warehouse infrastructure, we have now developed a Web app that facilitates FAIR for any index population. CONCLUSIONS: FAIR is a valuable research and clinical resource that extends the capabilities of existing data warehouses and lays the groundwork for family-based research. FAIR will expedite studies that would otherwise require registry or manual chart abstraction data sources

Use of the i2b2 research query tool to conduct a matched case–control clinical research study: advantages, disadvantages and methodological considerations

Background: A major aim of the i2b2 (informatics for integrating biology and the bedside) clinical data informatics framework aims to create an efficient structure within which patients can be identified for clinical and translational research projects. Our objective was to describe the respective roles of the i2b2 research query tool and the electronic medical record (EMR) in conducting a case-controlled clinical study at our institution. Methods: We analyzed the process of using i2b2 and the EMR together to generate a complete research database for a case–control study that sought to examine risk factors for kidney stones among gastrostomy tube (G-tube) fed children. Results: Our final case cohort consisted of 41/177 (23%) of potential cases initially identified by i2b2, who were matched with 80/486 (17%) of potential controls. Cases were 10 times more likely to be excluded for inaccurate coding regarding stones vs. inaccurate coding regarding G-tubes. A majority (67%) of cases were excluded due to not meeting clinical inclusion criteria, whereas a majority of control exclusions (72%) occurred due to inadequate clinical data necessary for study completion. Full dataset assembly required complementary information from i2b2 and the EMR. Conclusions: i2b2 was critical as a query analysis tool for patient identification in our case–control study. Patient identification via procedural coding appeared more accurate compared with diagnosis coding. Completion of our investigation required iterative interplay of i2b2 and the EMR to assemble the study cohort

Big Data as a Driver for Clinical Decision Support Systems: A Learning Health Systems Perspective

Big data technologies are nowadays providing health care with powerful instruments to gather and analyze large volumes of heterogeneous data collected for different purposes, including clinical care, administration, and research. This makes possible to design IT infrastructures that favor the implementation of the so-called "Learning Healthcare System Cycle," where healthcare practice and research are part of a unique and synergic process. In this paper we highlight how "Big Data enabled" integrated data collections may support clinical decision-making together with biomedical research. Two effective implementations are reported, concerning decision support in Diabetes and in Inherited Arrhythmogenic Diseases

Doctor of Philosophy

dissertationBiomedical data are a rich source of information and knowledge. Not only are they useful for direct patient care, but they may also offer answers to important population-based questions. Creating an environment where advanced analytics can be performed against biomedical data is nontrivial, however. Biomedical data are currently scattered across multiple systems with heterogeneous data, and integrating these data is a bigger task than humans can realistically do by hand; therefore, automatic biomedical data integration is highly desirable but has never been fully achieved. This dissertation introduces new algorithms that were devised to support automatic and semiautomatic integration of heterogeneous biomedical data. The new algorithms incorporate both data mining and biomedical informatics techniques to create "concept bags" that are used to compute similarity between data elements in the same way that "word bags" are compared in data mining. Concept bags are composed of controlled medical vocabulary concept codes that are extracted from text using named-entity recognition software. To test the new algorithm, three biomedical text similarity use cases were examined: automatically aligning data elements between heterogeneous data sets, determining degrees of similarity between medical terms using a published benchmark, and determining similarity between ICU discharge summaries. The method is highly configurable and 5 different versions were tested. The concept bag method performed particularly well aligning data elements and outperformed the compared algorithms by iv more than 5%. Another configuration that included hierarchical semantics performed particularly well at matching medical terms, meeting or exceeding 30 of 31 other published results using the same benchmark. Results for the third scenario of computing ICU discharge summary similarity were less successful. Correlations between multiple methods were low, including between terminologists. The concept bag algorithms performed consistently and comparatively well and appear to be viable options for multiple scenarios. New applications of the method and ideas for improving the algorithm are being discussed for future work, including several performance enhancements, configuration-based enhancements, and concept vector weighting using the TF-IDF formulas