Semantic Web

The role of ontologies in biological and biomedical research: a functional perspective.

Fri, 2016-09-16 08:52
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The role of ontologies in biological and biomedical research: a functional perspective.

Brief Bioinform. 2015 Nov;16(6):1069-80

Authors: Hoehndorf R, Schofield PN, Gkoutos GV

Abstract
Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

PMID: 25863278 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

Large-scale Cross-modality Search via Collective Matrix Factorization Hashing.

Wed, 2016-09-14 08:17
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Large-scale Cross-modality Search via Collective Matrix Factorization Hashing.

IEEE Trans Image Process. 2016 Sep 8;

Authors: Ding G, Guo Y, Zhou J, Gao Y

Abstract
By transforming data into binary representation, i.e., Hashing, we can perform high-speed search with low storage cost, and thus Hashing has collected increasing research interest in the recent years. Recently, how to generate Hashcode for multimodal data (e.g., images with textual tags, documents with photos, etc) for large-scale cross-modality search (e.g., searching semantically related images in database for a document query) is an important research issue because of the fast growth of multimodal data in the Web. To address this issue, a novel framework for multimodal Hashing is proposed, termed as Collective Matrix Factorization Hashing (CMFH). The key idea of CMFH is to learn unified Hashcodes for different modalities of one multimodal instance in the shared latent semantic space in which different modalities can be effectively connected. Therefore, accurate cross-modality search is supported. Based on the general framework, we extend it in the unsupervised scenario where it tries to preserve the Euclidean structure, and in the supervised scenario where it fully exploits the label information of data. The corresponding theoretical analysis and the optimization algorithms are given. We conducted comprehensive experiments on three benchmark datasets for cross-modality search. The experimental results demonstrate that CMFH can significantly outperform several state-of-the-art cross-modality Hashing methods, which validates the effectiveness of the proposed CMFH.

PMID: 27623584 [PubMed - as supplied by publisher]

Categories: Literature Watch

FoodWiki: a Mobile App Examines Side Effects of Food Additives Via Semantic Web.

Tue, 2016-09-13 08:00
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FoodWiki: a Mobile App Examines Side Effects of Food Additives Via Semantic Web.

J Med Syst. 2016 Feb;40(2):41

Authors: Çelik Ertuğrul D

Abstract
In this article, a research project on mobile safe food consumption system (FoodWiki) is discussed that performs its own inferencing rules in its own knowledge base. Currently, the developed rules examines the side effects that are causing some health risks: heart disease, diabetes, allergy, and asthma as initial. There are thousands compounds added to the processed food by food producers with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. Those commonly used ingredients or compounds in manufactured foods may have many side effects that cause several health risks such as heart disease, hypertension, cholesterol, asthma, diabetes, allergies, alzheimer etc. according to World Health Organization. Safety in food consumption, especially by patients in these risk groups, has become crucial, given that such health problems are ranked in the top ten health risks around the world. It is needed personal e-health knowledge base systems to help patients take control of their safe food consumption. The systems with advanced semantic knowledge base can provide recommendations of appropriate foods before consumption by individuals. The proposed FoodWiki system is using a concept based search mechanism that performs on thousands food compounds to provide more relevant information.

PMID: 26590979 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets.

Sat, 2016-09-10 07:12
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Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets.

BMC Genomics. 2015;16:1071

Authors: Klus P, Ponti RD, Livi CM, Tartaglia GG

Abstract
BACKGROUND: Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discriminate multiple protein datasets (multiCM) and to measure enrichments in gene ontology terms (cleverGO) using semantic similarities.
RESULTS: We illustrate the powerfulness of our approach by investigating the links between RNA-binding ability and other protein features, such as structural disorder and aggregation, in S. cerevisiae, C. elegans, M. musculus and H. sapiens. Our results are in striking agreement with available experimental evidence and unravel features that are key to understand the mechanisms regulating cellular homeostasis.
CONCLUSIONS: In an intuitive way, multiCM and cleverGO provide accurate classifications of physico-chemical features and annotations of biological processes, molecular functions and cellular components, which is extremely useful for the discovery and characterization of new trends in protein datasets. The multiCM and cleverGO can be freely accessed on the Web at http://www.tartaglialab.com/cs_multi/submission and http://www.tartaglialab.com/GO_analyser/universal . Each of the pages contains links to the corresponding documentation and tutorial.

PMID: 26673865 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

The health care and life sciences community profile for dataset descriptions.

Thu, 2016-09-08 06:36

The health care and life sciences community profile for dataset descriptions.

PeerJ. 2016;4:e2331

Authors: Dumontier M, Gray AJ, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A

Abstract
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

PMID: 27602295 [PubMed]

Categories: Literature Watch

Exploiting Semantic Web Technologies to Develop OWL-Based Clinical Practice Guideline Execution Engines.

Wed, 2016-09-07 06:12
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Exploiting Semantic Web Technologies to Develop OWL-Based Clinical Practice Guideline Execution Engines.

IEEE J Biomed Health Inform. 2016 Jan;20(1):388-98

Authors: Jafarpour B, Abidi SR, Abidi SS

Abstract
Computerizing paper-based CPG and then executing them can provide evidence-informed decision support to physicians at the point of care. Semantic web technologies especially web ontology language (OWL) ontologies have been profusely used to represent computerized CPG. Using semantic web reasoning capabilities to execute OWL-based computerized CPG unties them from a specific custom-built CPG execution engine and increases their shareability as any OWL reasoner and triple store can be utilized for CPG execution. However, existing semantic web reasoning-based CPG execution engines suffer from lack of ability to execute CPG with high levels of expressivity, high cognitive load of computerization of paper-based CPG and updating their computerized versions. In order to address these limitations, we have developed three CPG execution engines based on OWL 1 DL, OWL 2 DL and OWL 2 DL + semantic web rule language (SWRL). OWL 1 DL serves as the base execution engine capable of executing a wide range of CPG constructs, however for executing highly complex CPG the OWL 2 DL and OWL 2 DL + SWRL offer additional executional capabilities. We evaluated the technical performance and medical correctness of our execution engines using a range of CPG. Technical evaluations show the efficiency of our CPG execution engines in terms of CPU time and validity of the generated recommendation in comparison to existing CPG execution engines. Medical evaluations by domain experts show the validity of the CPG-mediated therapy plans in terms of relevance, safety, and ordering for a wide range of patient scenarios.

PMID: 25532198 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

Sat, 2016-09-03 06:52

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

BMC Genomics. 2016;17 Suppl 5:530

Authors: Peng J, Li H, Liu Y, Juan L, Jiang Q, Wang Y, Chen J

Abstract
BACKGROUND: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation.
RESULTS: We present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks.
CONCLUSIONS: InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .

PMID: 27586009 [PubMed - in process]

Categories: Literature Watch

Designing a patient monitoring system for bipolar disorder using Semantic Web technologies.

Fri, 2016-09-02 06:17
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Designing a patient monitoring system for bipolar disorder using Semantic Web technologies.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:6788-91

Authors: Thermolia C, Bei ES, Petrakis EG, Kritsotakis V, Tsiknakis M, Sakkalis V

Abstract
The new movement to personalize treatment plans and improve prediction capabilities is greatly facilitated by intelligent remote patient monitoring and risk prevention. This paper focuses on patients suffering from bipolar disorder, a mental illness characterized by severe mood swings. We exploit the advantages of Semantic Web and Electronic Health Record Technologies to develop a patient monitoring platform to support clinicians. Relying on intelligently filtering of clinical evidence-based information and individual-specific knowledge, we aim to provide recommendations for treatment and monitoring at appropriate time or concluding into alerts for serious shifts in mood and patients' non response to treatment.

PMID: 26737852 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

Dynamic User Interfaces for Service Oriented Architectures in Healthcare.

Thu, 2016-09-01 08:45
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Dynamic User Interfaces for Service Oriented Architectures in Healthcare.

Stud Health Technol Inform. 2016;228:795-7

Authors: Schweitzer M, Hoerbst A

Abstract
Electronic Health Records (EHRs) play a crucial role in healthcare today. Considering a data-centric view, EHRs are very advanced as they provide and share healthcare data in a cross-institutional and patient-centered way adhering to high syntactic and semantic interoperability. However, the EHR functionalities available for the end users are rare and hence often limited to basic document query functions. Future EHR use necessitates the ability to let the users define their needed data according to a certain situation and how this data should be processed. Workflow and semantic modelling approaches as well as Web services provide means to fulfil such a goal. This thesis develops concepts for dynamic interfaces between EHR end users and a service oriented eHealth infrastructure, which allow the users to design their flexible EHR needs, modeled in a dynamic and formal way. These are used to discover, compose and execute the right Semantic Web services.

PMID: 27577496 [PubMed - in process]

Categories: Literature Watch

A Digital Health System to Assist Family Physicians to Safely Prescribe NOAC Medications.

Thu, 2016-09-01 08:45
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A Digital Health System to Assist Family Physicians to Safely Prescribe NOAC Medications.

Stud Health Technol Inform. 2016;228:519-23

Authors: Abidi SR, Cox J, Abusharekh A, Hashemian N, Abidi SS

Abstract
Atrial Fibrillation (AF) is the most common cardiac arrhythmia. Generally, the therapeutic options for managing AF include the use of anticoagulant drugs that prevent the coagulation of blood. New Oral Anticoagulants (NOACs) are not optimally prescribed to patients, despite their efficacy. In Canada, NOAC medications are not directly available to patients who belong to provincial benefits programs, rather a NOAC special authorization process establishes the eligibility of a patient to receive a NOAC and be paid by the provincial Pharmacare program. This special authorization process is tedious and paper-based which inhibits physicians to prescribe NOAC leading to suboptimal AF care to patients. In this paper, we present a computerized NOAC Authorization Decision Support System (NOAC-ADSS), accessible to physicians to help them (a) determine a patient eligibility for NOAC based on Canadian AF clinical guidelines, and (b) complete the special authorization form. We present a semantic web based system to ontologically model the NOAC eligibility criteria and execute the knowledge to determine a patient NOAC eligibility and dosage.

PMID: 27577437 [PubMed - in process]

Categories: Literature Watch

Thesaurus-Based Hierarchical Semantic Grouping of Medical Terms in Information Extraction.

Thu, 2016-09-01 08:45
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Thesaurus-Based Hierarchical Semantic Grouping of Medical Terms in Information Extraction.

Stud Health Technol Inform. 2016;228:446-50

Authors: Lassoued Y, Deleris L

Abstract
In this paper we describe a semantic approach for grouping medical terms into a hierarchy of concepts based on the UMLS meta-thesaurus. The context of this work is Medical Recap, a Web system that automatically extracts risk information from PubMed abstracts, and then aggregates this knowledge into dependence graphs or Bayesian networks.

PMID: 27577422 [PubMed - in process]

Categories: Literature Watch

An Ontological Model of Behaviour Theory to Generate Personalized Action Plans to Modify Behaviours.

Thu, 2016-09-01 08:45
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An Ontological Model of Behaviour Theory to Generate Personalized Action Plans to Modify Behaviours.

Stud Health Technol Inform. 2016;228:399-403

Authors: Baig W, Abidi S, Abidi SS

Abstract
Behavior change approaches aim to assist patients in achieving self-efficacy in managing their condition. Social cognitive theory (SCT) stipulates self-efficacy as a central element to behavior change and provides constructs to achieve self-efficacy guided by person-specific action plans. In our work, to administer behaviour change in patient with chronic conditions, our approach entails the computerization of SCT-based self-efficacy constructs in order to generate personalized action plans that are suitable to an individual's current care scenario. We have taken a knowledge management approach, whereby we have computerized the SCT-based self-efficacy constructs in terms of a high-level SCT knowledge model that can be operationalized to generate personalized behaviour change action plans. We have collected and computerized behavior change content targeting healthy living and physical activity. Semantic web technologies have been used to develop the SCT knowledge model, represented in terms of an ontology and SWRL rules. The ontological SCT model can inferred to generate personalized self-management action plans for a given patient profile. We present formative evaluation of the clinical correctness and relevance of the generated personalized action plans for a range of test patient profiles.

PMID: 27577412 [PubMed - in process]

Categories: Literature Watch

Building a Semantic Model to Enhance the User's Perceived Functionality of the EHR.

Thu, 2016-09-01 08:45
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Building a Semantic Model to Enhance the User's Perceived Functionality of the EHR.

Stud Health Technol Inform. 2016;228:137-41

Authors: Lasierra N, Schweitzer M, Gorfer T, Toma I, Hoerbst A

Abstract
In order to facilitate and increase the usability of Electronic Health Records (EHRs) for healthcare professional's daily work, we have designed a system that enables functional and flexible EHR access, based on the execution of clinical workflows and the composition of Semantic Web Services (SWS). The backbone of this system is based on an ontology. In this paper we present the strategy that we have followed for its design, and an overview of the resulting model. The designed ontology enables to model patient-centred clinical EHR workflows, the involved sequence of tasks and its associated functionality and managed clinical data. This semantic model constitutes also the main pillar for enabling dynamic service selection in our system.

PMID: 27577358 [PubMed - in process]

Categories: Literature Watch

A National Medical Information System for Senegal: Architecture and Services.

Thu, 2016-09-01 08:45
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A National Medical Information System for Senegal: Architecture and Services.

Stud Health Technol Inform. 2016;228:43-7

Authors: Camara G, Diallo AH, Lo M, Tendeng JN, Lo S

Abstract
In Senegal, great amounts of data are daily generated by medical activities such as consultation, hospitalization, blood test, x-ray, birth, death, etc. These data are still recorded in register, printed images, audios and movies which are manually processed. However, some medical organizations have their own software for non-standardized patient record management, appointment, wages, etc. without any possibility of sharing these data or communicating with other medical structures. This leads to lots of limitations in reusing or sharing these data because of their possible structural and semantic heterogeneity. To overcome these problems we have proposed a National Medical Information System for Senegal (SIMENS). As an integrated platform, SIMENS provides an EHR system that supports healthcare activities, a mobile version and a web portal. The SIMENS architecture proposes also a data and application integration services for supporting interoperability and decision making.

PMID: 27577338 [PubMed - in process]

Categories: Literature Watch

Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing.

Tue, 2016-08-30 08:13

Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing.

AMIA Jt Summits Transl Sci Proc. 2016;2016:132-9

Authors: Liang C, Sun J, Tao C

Abstract
Despite ongoing progress towards treating mental illness, there remain significant difficulties in selecting probable candidate drugs from the existing database. We describe an ontology - oriented approach aims to represent the nexus between genes, drugs, phenotypes, symptoms, and diseases from multiple information sources. Along with this approach, we report a case study in which we attempted to explore the candidate drugs that effective for both bipolar disorder and epilepsy. We constructed an ontology that incorporates the knowledge between the two diseases and performed semantic reasoning task on the ontology. The reasoning results suggested 48 candidate drugs that hold promise for a further breakthrough. The evaluation was performed and demonstrated the validity of the proposed ontology. The overarching goal of this research is to build a framework of ontology - based data integration underpinning psychiatric drug repurposing. This approach prioritizes the candidate drugs that have potential associations among genes, phenotypes and symptoms, and thus facilitates the data integration and drug repurposing in psychiatric disorders.

PMID: 27570661 [PubMed]

Categories: Literature Watch

Integrating semantic dimension into openEHR archetypes for the management of cerebral palsy electronic medical records.

Mon, 2016-08-29 08:02

Integrating semantic dimension into openEHR archetypes for the management of cerebral palsy electronic medical records.

J Biomed Inform. 2016 Aug 24;

Authors: Ellouze AS, Bouaziz R, Ghorbel H

Abstract
PURPOSE: Integrating semantic dimension into clinical archetypes is necessary once modeling medical records. First, it enables semantic interoperability and, it offers applying semantic activities on clinical data and provides a higher design quality of Electronic Medical Record (EMR) systems. However, to obtain these advantages, designers need to use archetypes that cover semantic features of clinical concepts involved in their specific applications. In fact, most of archetypes filed within open repositories are expressed in the Archetype Definition Language (ALD) which allows defining only the syntactic structure of clinical concepts weakening semantic activities on the EMR content in the semantic web environment. This paper focuses on the modeling of an EMR prototype for infants affected by Cerebral Palsy (CP), using the dual model approach and integrating semantic web technologies. Such a modeling provides a better delivery of quality of care and ensures semantic interoperability between all involved therapies' information systems.
METHODS: First, data to be documented are identified and collected from the involved therapies. Subsequently, data are analyzed and arranged into archetypes expressed in accordance of ADL. During this step, open archetype repositories are explored, in order to find the suitable archetypes. Then, ADL archetypes are transformed into archetypes expressed in OWL-DL (Ontology Web Language - Description Language). Finally, we construct an ontological source related to these archetypes enabling hence their annotation to facilitate data extraction and providing possibility to exercise semantic activities on such archetypes.
RESULTS: Semantic dimension integration into EMR modeled in accordance to the archetype approach. The feasibility of our solution is shown through the development of a prototype, baptized "CP-SMS", which ensures semantic exploitation of CP EMR. This prototype provides the following features: (i) creation of CP EMR instances and their checking by using a knowledge base which we have constructed by interviews with domain experts, (ii) translation of initially CP ADL archetypes into CP OWL-DL archetypes, (iii) creation of an ontological source which we can use to annotate obtained archetypes and (vi) enrichment and supply of the ontological source and integration of semantic relations by providing hence fueling the ontology with new concepts, ensuring consistency and eliminating ambiguity between concepts.
CONCLUSIONS: The degree of semantic interoperability that could be reached between EMR systems depends strongly on the quality of the used archetypes. Thus, the integration of semantic dimension in archetypes modeling process is crucial. By creating an ontological source and annotating archetypes, we create a supportive platform ensuring semantic interoperability between archetypes-based EMR-systems.

PMID: 27568295 [PubMed - as supplied by publisher]

Categories: Literature Watch

Designing a CTSA-Based Social Network Intervention to Foster Cross-Disciplinary Team Science.

Tue, 2016-08-23 06:30
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Designing a CTSA-Based Social Network Intervention to Foster Cross-Disciplinary Team Science.

Clin Transl Sci. 2015 Aug;8(4):281-9

Authors: Vacca R, McCarty C, Conlon M, Nelson DR

Abstract
This paper explores the application of network intervention strategies to the problem of assembling cross-disciplinary scientific teams in academic institutions. In a project supported by the University of Florida (UF) Clinical and Translational Science Institute, we used VIVO, a semantic-web research networking system, to extract the social network of scientific collaborations on publications and awarded grants across all UF colleges and departments. Drawing on the notion of network interventions, we designed an alteration program to add specific edges to the collaboration network, that is, to create specific collaborations between previously unconnected investigators. The missing collaborative links were identified by a number of network criteria to enhance desirable structural properties of individual positions or the network as a whole. We subsequently implemented an online survey (N = 103) that introduced the potential collaborators to each other through their VIVO profiles, and investigated their attitudes toward starting a project together. We discuss the design of the intervention program, the network criteria adopted, and preliminary survey results. The results provide insight into the feasibility of intervention programs on scientific collaboration networks, as well as suggestions on the implementation of such programs to assemble cross-disciplinary scientific teams in CTSA institutions.

PMID: 25788258 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

Extraction of a group-pair relation: problem-solving relation from web-board documents.

Sat, 2016-08-20 08:47

Extraction of a group-pair relation: problem-solving relation from web-board documents.

Springerplus. 2016;5(1):1265

Authors: Pechsiri C, Piriyakul R

Abstract
This paper aims to extract a group-pair relation as a Problem-Solving relation, for example a DiseaseSymptom-Treatment relation and a CarProblem-Repair relation, between two event-explanation groups, a problem-concept group as a symptom/CarProblem-concept group and a solving-concept group as a treatment-concept/repair concept group from hospital-web-board and car-repair-guru-web-board documents. The Problem-Solving relation (particularly Symptom-Treatment relation) including the graphical representation benefits non-professional persons by supporting knowledge of primarily solving problems. The research contains three problems: how to identify an EDU (an Elementary Discourse Unit, which is a simple sentence) with the event concept of either a problem or a solution; how to determine a problem-concept EDU boundary and a solving-concept EDU boundary as two event-explanation groups, and how to determine the Problem-Solving relation between these two event-explanation groups. Therefore, we apply word co-occurrence to identify a problem-concept EDU and a solving-concept EDU, and machine-learning techniques to solve a problem-concept EDU boundary and a solving-concept EDU boundary. We propose using k-mean and Naïve Bayes to determine the Problem-Solving relation between the two event-explanation groups involved with clustering features. In contrast to previous works, the proposed approach enables group-pair relation extraction with high accuracy.

PMID: 27540498 [PubMed]

Categories: Literature Watch

Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies.

Fri, 2016-08-19 08:34
Related Articles

Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies.

Biomed Res Int. 2015;2015:976272

Authors: Sinaci AA, Laleci Erturkmen GB, Gonul S, Yuksel M, Invernizzi P, Thakrar B, Pacaci A, Cinar HA, Cicekli NK

Abstract
Postmarketing drug surveillance is a crucial aspect of the clinical research activities in pharmacovigilance and pharmacoepidemiology. Successful utilization of available Electronic Health Record (EHR) data can complement and strengthen postmarketing safety studies. In terms of the secondary use of EHRs, access and analysis of patient data across different domains are a critical factor; we address this data interoperability problem between EHR systems and clinical research systems in this paper. We demonstrate that this problem can be solved in an upper level with the use of common data elements in a standardized fashion so that clinical researchers can work with different EHR systems independently of the underlying information model. Postmarketing Safety Study Tool lets the clinical researchers extract data from different EHR systems by designing data collection set schemas through common data elements. The tool interacts with a semantic metadata registry through IHE data element exchange profile. Postmarketing Safety Study Tool and its supporting components have been implemented and deployed on the central data warehouse of the Lombardy region, Italy, which contains anonymized records of about 16 million patients with over 10-year longitudinal data on average. Clinical researchers in Roche validate the tool with real life use cases.

PMID: 26543873 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

From Cues to Nudge: A Knowledge-Based Framework for Surveillance of Healthcare-Associated Infections.

Thu, 2016-08-18 08:12
Related Articles

From Cues to Nudge: A Knowledge-Based Framework for Surveillance of Healthcare-Associated Infections.

J Med Syst. 2016 Jan;40(1):23

Authors: Shaban-Nejad A, Mamiya H, Riazanov A, Forster AJ, Baker CJ, Tamblyn R, Buckeridge DL

Abstract
We propose an integrated semantic web framework consisting of formal ontologies, web services, a reasoner and a rule engine that together recommend appropriate level of patient-care based on the defined semantic rules and guidelines. The classification of healthcare-associated infections within the HAIKU (Hospital Acquired Infections - Knowledge in Use) framework enables hospitals to consistently follow the standards along with their routine clinical practice and diagnosis coding to improve quality of care and patient safety. The HAI ontology (HAIO) groups over thousands of codes into a consistent hierarchy of concepts, along with relationships and axioms to capture knowledge on hospital-associated infections and complications with focus on the big four types, surgical site infections (SSIs), catheter-associated urinary tract infection (CAUTI); hospital-acquired pneumonia, and blood stream infection. By employing statistical inferencing in our study we use a set of heuristics to define the rule axioms to improve the SSI case detection. We also demonstrate how the occurrence of an SSI is identified using semantic e-triggers. The e-triggers will be used to improve our risk assessment of post-operative surgical site infections (SSIs) for patients undergoing certain type of surgeries (e.g., coronary artery bypass graft surgery (CABG)).

PMID: 26537131 [PubMed - indexed for MEDLINE]

Categories: Literature Watch

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