Exploring biomedical ontology mappings with graph theory methods.

PeerJ. 2017;5:e2990

Authors: Kocbek S, Kim JD

Abstract
BACKGROUND: In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies.
METHODS: We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature.
RESULTS: With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

PMID: 28265499 [PubMed - in process]

BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

Comput Methods Programs Biomed. 2016 Jul;131:63-77

Authors: Jácome AG, Fdez-Riverola F, Lourenço A

Abstract
BACKGROUND AND OBJECTIVES: Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces.
METHODS: The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization.
RESULTS: The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results, and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations.
CONCLUSIONS: The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibilityin terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts. The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef.

PMID: 27265049 [PubMed - indexed for MEDLINE]

Text mining for improved exposure assessment.

PLoS One. 2017;12(3):e0173132

Authors: Larsson K, Baker S, Silins I, Guo Y, Stenius U, Korhonen A, Berglund M

Abstract
Chemical exposure assessments are based on information collected via different methods, such as biomonitoring, personal monitoring, environmental monitoring and questionnaires. The vast amount of chemical-specific exposure information available from web-based databases, such as PubMed, is undoubtedly a great asset to the scientific community. However, manual retrieval of relevant published information is an extremely time consuming task and overviewing the data is nearly impossible. Here, we present the development of an automatic classifier for chemical exposure information. First, nearly 3700 abstracts were manually annotated by an expert in exposure sciences according to a taxonomy exclusively created for exposure information. Natural Language Processing (NLP) techniques were used to extract semantic and syntactic features relevant to chemical exposure text. Using these features, we trained a supervised machine learning algorithm to automatically classify PubMed abstracts according to the exposure taxonomy. The resulting classifier demonstrates good performance in the intrinsic evaluation. We also show that the classifier improves information retrieval of chemical exposure data compared to keyword-based PubMed searches. Case studies demonstrate that the classifier can be used to assist researchers by facilitating information retrieval and classification, enabling data gap recognition and overviewing available scientific literature using chemical-specific publication profiles. Finally, we identify challenges to be addressed in future development of the system.

PMID: 28257498 [PubMed - in process]

Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience.

Front Neuroinform. 2017;11:12

Authors: Matiasz NJ, Wood J, Wang W, Silva AJ, Hsu W

Abstract
Computers help neuroscientists to analyze experimental results by automating the application of statistics; however, computer-aided experiment planning is far less common, due to a lack of similar quantitative formalisms for systematically assessing evidence and uncertainty. While ontologies and other Semantic Web resources help neuroscientists to assimilate required domain knowledge, experiment planning requires not only ontological but also epistemological (e.g., methodological) information regarding how knowledge was obtained. Here, we outline how epistemological principles and graphical representations of causality can be used to formalize experiment planning toward causal discovery. We outline two complementary approaches to experiment planning: one that quantifies evidence per the principles of convergence and consistency, and another that quantifies uncertainty using logical representations of constraints on causal structure. These approaches operationalize experiment planning as the search for an experiment that either maximizes evidence or minimizes uncertainty. Despite work in laboratory automation, humans must still plan experiments and will likely continue to do so for some time. There is thus a great need for experiment-planning frameworks that are not only amenable to machine computation but also useful as aids in human reasoning.

PMID: 28243197 [PubMed - in process]

Biological aspects and candidate biomarkers for psychotic bipolar disorder: A systematic review.

Psychiatry Clin Neurosci. 2016 Jun;70(6):227-44

Authors: Buoli M, Caldiroli A, Cumerlato Melter C, Serati M, de Nijs J, Altamura AC

Abstract
AIM: We carried out a systematic review of the available literature about potential biomarkers of psychotic bipolar disorder (BD-P), a specific subset presenting worse outcome and greater risk of relapse than non-psychotic bipolar disorder (BD-NP).
METHODS: We searched the main psychiatric databases (PubMed, ISI Web of Knowledge, PsychInfo). Only original articles with the main topic of BD-P compared to schizophrenia/BD-NP/healthy controls (HC) written in English from 1994 to 2015 were included.
RESULTS: BD-P patients presented higher kynurenic acid levels in the cerebrospinal fluid, elevated anti- S accharomyces cerevisiae antibodies levels, and lower serum levels of dehydroepiandrosterone sulfate and progesterone than BD-NP/HC. Event-related potentials abnormalities have been identified in BD-P with respect to BD-NP. BD-P patients also presented bigger ventricles but similar hippocampal volumes compared to BD-NP/HC. Although the results are contrasting, some cognitive deficits seemed to be related to the psychotic dimension of bipolar affective disorder, such as impairment in verbal/logical memory, working memory, verbal and semantic fluency and executive functioning. Finally, polymorphisms of genes, such as NRG1, 5HTTLPR (s), COMT, DAOA and some chromosome regions (16p12 and 13q), were positively associated with BD-P.
CONCLUSION: Data about the identification of specific biomarkers for BD-P are promising, but most of them have not yet been replicated. They could lead the clinicians to an early diagnosis and proper treatment, thus ameliorating outcome of BD-P and reducing the biological changes associated with a long duration of illness. Further studies with bigger samples are needed to detect more specific biological markers of the psychotic dimension of bipolar affective disorder.

PMID: 26969211 [PubMed - indexed for MEDLINE]

Neuropsychological performance changes following subthalamic versus pallidal deep brain stimulation in Parkinson's disease: a systematic review and metaanalysis.

CNS Spectr. 2017 Feb 27;:1-14

Authors: Elgebaly A, Elfil M, Attia A, Magdy M, Negida A

Abstract
BACKGROUND: Studies comparing subthalamus (STN) and globus pallidus internus (GPi) deep brain stimulation (DBS) for the management of Parkinson's disease in terms of neuropsychological performance are scarce and heterogeneous. Therefore, we performed a systematic review and metaanalysis to compare neuropsychological outcomes following STN DBS versus GPi DBS.
METHODS: A computer literature search of PubMed, the Web of Science, and Cochrane Central was conducted. Records were screened for eligible studies, and data were extracted and synthesized using Review Manager (v. 5.3 for Windows).
RESULTS: Seven studies were included in the qualitative synthesis. Of them, four randomized controlled trials (n=345 patients) were pooled in the metaanalysis models. The standardized mean difference (SMD) of change in the Stroop color-naming test favored the GPi DBS group (SMD=-0.31, p=0.009). However, other neuropsychological outcomes did not favor either of the two groups (Stroop word-reading: SMD=-0.21, p=0.08; the Wechsler Adult Intelligence Scale (WAIS) digits forward: SMD=0.08, p=0.47; Trail Making Test Part A: SMD=-0.05, p=0.65; WAIS-R digit symbol: SMD=-0.16, p=0.29; Trail Making Test Part B: SMD=-0.14, p=0.23; Stroop color-word interference: SMD=-0.16, p=0.18; phonemic verbal fluency: bilateral DBS SMD=-0.04, p=0.73, and unilateral DBS SMD=-0.05, p=0.83; semantic verbal fluency: bilateral DBS SMD=-0.09, p=0.37, and unilateral DBS SMD=-0.29, p=0.22; Boston Naming Test: SMD=-0.11, p=0.33; Beck Depression Inventory: bilateral DBS SMD=0.15, p=0.31, and unilateral DBS SMD=0.36, p=0.11).
CONCLUSIONS: There was no statistically significant difference in most of the neuropsychological outcomes. The present evidence does not favor any of the targets in terms of neuropsychological performance.

PMID: 28236811 [PubMed - as supplied by publisher]

Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System.

Sensors (Basel). 2017 Feb 20;17(2):

Authors: Wu Z, Xu Y, Yang Y, Zhang C, Zhu X, Ji Y

Abstract
Web of Things (WoT) facilitates the discovery and interoperability of Internet of Things (IoT) devices in a cyber-physical system (CPS). Moreover, a uniform knowledge representation of physical resources is quite necessary for further composition, collaboration, and decision-making process in CPS. Though several efforts have integrated semantics with WoT, such as knowledge engineering methods based on semantic sensor networks (SSN), it still could not represent the complex relationships between devices when dynamic composition and collaboration occur, and it totally depends on manual construction of a knowledge base with low scalability. In this paper, to addresses these limitations, we propose the semantic Web of Things (SWoT) framework for CPS (SWoT4CPS). SWoT4CPS provides a hybrid solution with both ontological engineering methods by extending SSN and machine learning methods based on an entity linking (EL) model. To testify to the feasibility and performance, we demonstrate the framework by implementing a temperature anomaly diagnosis and automatic control use case in a building automation system. Evaluation results on the EL method show that linking domain knowledge to DBpedia has a relative high accuracy and the time complexity is at a tolerant level. Advantages and disadvantages of SWoT4CPS with future work are also discussed.

PMID: 28230725 [PubMed - in process]

Tashkeela: Novel corpus of Arabic vocalized texts, data for auto-diacritization systems.

Data Brief. 2017 Apr;11:147-151

Authors: Zerrouki T, Balla A

Abstract
Arabic diacritics are often missed in Arabic scripts. This feature is a handicap for new learner to read َArabic, text to speech conversion systems, reading and semantic analysis of Arabic texts. The automatic diacritization systems are the best solution to handle this issue. But such automation needs resources as diactritized texts to train and evaluate such systems. In this paper, we describe our corpus of Arabic diacritized texts. This corpus is called Tashkeela. It can be used as a linguistic resource tool for natural language processing such as automatic diacritics systems, dis-ambiguity mechanism, features and data extraction. The corpus is freely available, it contains 75 million of fully vocalized words mainly 97 books from classical and modern Arabic language. The corpus is collected from manually vocalized texts using web crawling process.

PMID: 28224131 [PubMed - in process]

SCALEUS: Semantic Web Services Integration for Biomedical Applications.

J Med Syst. 2017 Apr;41(4):54

Authors: Sernadela P, González-Castro L, Oliveira JL

Abstract
In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

PMID: 28214993 [PubMed - in process]

Modeling and Validating HL7 FHIR Profiles Using Semantic Web Shape Expressions (ShEx).

J Biomed Inform. 2017 Feb 14;:

Authors: Solbrig HR, Prud'hommeaux E, Grieve G, McKenzie L, Mandel JC, Sharma DK, Jiang G

Abstract
BACKGROUND: HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation.
OBJECTIVE: Create a FHIR to ShEx model transformation and assess its ability to describe and validate FHIR RDF data.
METHODS: We created the methods and tools that generate the ShEx schemas modeling the FHIR to RDF specification being developed by HL7 ITS/W3C RDF Task Force, and evaluated the applicability of ShEx in the description and validation of FHIR to RDF transformations.
RESULTS: The ShEx models contributed significantly to workgroup consensus. Algorithmic transformations from the FHIR model to ShEx schemas and FHIR example data to RDF transformations were incorporated into the FHIR build process. ShEx schemas representing 109 FHIR resources were used to validate 511 FHIR RDF data examples from the Standards for Trial Use (STU 3) Ballot version. We were able to uncover unresolved issues in the FHIR to RDF specification and detect 10 types of errors and root causes in the actual implementation. The FHIR ShEx representations have been included in the official FHIR web pages for the STU 3 Ballot version since September 2016.
DISCUSSION: ShEx can be used to define and validate the syntax of a FHIR resource, which is complementary to the use of RDF Schema (RDFS) and Web Ontology Language (OWL) for semantic validation.
CONCLUSION: ShEx proved useful for describing a standard model of FHIR RDF data. The combination of a formal model and a succinct format enabled comprehensive review and automated validation.

PMID: 28213144 [PubMed - as supplied by publisher]

Semantics-based plausible reasoning to extend the knowledge coverage of medical knowledge bases for improved clinical decision support.

BioData Min. 2017;10:7

Authors: Mohammadhassanzadeh H, Van Woensel W, Abidi SR, Abidi SS

Abstract
BACKGROUND: Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians' experiences. To extend the coverage of incomplete medical knowledge-based systems beyond their deductive closure, and thus enhance their decision-support capabilities, we argue that innovative, multi-strategy reasoning approaches should be applied. In particular, plausible reasoning mechanisms apply patterns from human thought processes, such as generalization, similarity and interpolation, based on attributional, hierarchical, and relational knowledge. Plausible reasoning mechanisms include inductive reasoning, which generalizes the commonalities among the data to induce new rules, and analogical reasoning, which is guided by data similarities to infer new facts. By further leveraging rich, biomedical Semantic Web ontologies to represent medical knowledge, both known and tentative, we increase the accuracy and expressivity of plausible reasoning, and cope with issues such as data heterogeneity, inconsistency and interoperability. In this paper, we present a Semantic Web-based, multi-strategy reasoning approach, which integrates deductive and plausible reasoning and exploits Semantic Web technology to solve complex clinical decision support queries.
RESULTS: We evaluated our system using a real-world medical dataset of patients with hepatitis, from which we randomly removed different percentages of data (5%, 10%, 15%, and 20%) to reflect scenarios with increasing amounts of incomplete medical knowledge. To increase the reliability of the results, we generated 5 independent datasets for each percentage of missing values, which resulted in 20 experimental datasets (in addition to the original dataset). The results show that plausibly inferred knowledge extends the coverage of the knowledge base by, on average, 2%, 7%, 12%, and 16% for datasets with, respectively, 5%, 10%, 15%, and 20% of missing values. This expansion in the KB coverage allowed solving complex disease diagnostic queries that were previously unresolvable, without losing the correctness of the answers. However, compared to deductive reasoning, data-intensive plausible reasoning mechanisms yield a significant performance overhead.
CONCLUSIONS: We observed that plausible reasoning approaches, by generating tentative inferences and leveraging domain knowledge of experts, allow us to extend the coverage of medical knowledge bases, resulting in improved clinical decision support. Second, by leveraging OWL ontological knowledge, we are able to increase the expressivity and accuracy of plausible reasoning methods. Third, our approach is applicable to clinical decision support systems for a range of chronic diseases.

PMID: 28203277 [PubMed]

DaTo: an atlas of biological databases and tools.

J Integr Bioinform. 2016 Dec 18;13(4):297

Authors: Li Q, Zhou Y, Jiao Y, Zhang Z, Bai L, Tong L, Yang X, Sommer B, Hofestädt R, Chen M

Abstract
This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity. Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the last 20 years. We hope it will inspire the biological community to gain a systematic insight into bioinformatics resources. DaTo is accessible via http://bis.zju.edu.cn/DaTo/.

PMID: 28187413 [PubMed - in process]

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

BMC Bioinformatics. 2017 Feb 08;18(1):93

Authors: Chiba H, Uchiyama I

Abstract
BACKGROUND: Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary.
RESULTS: We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data.
CONCLUSIONS: SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

PMID: 28178937 [PubMed - in process]

An improved method for functional similarity analysis of genes based on Gene Ontology.

BMC Syst Biol. 2016 Dec 23;10(Suppl 4):119

Authors: Tian Z, Wang C, Guo M, Liu X, Teng Z

Abstract
BACKGROUND: Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional similarity methods have been proposed based on the semantic similarity of GO terms. However, these leading approaches may make errorprone judgments especially when they measure the specificity of GO terms as well as the IC of a term set. Therefore, how to estimate the gene functional similarity reliably is still a challenging problem.
RESULTS: We propose WIS, an effective method to measure the gene functional similarity. First of all, WIS computes the IC of a term by employing its depth, the number of its ancestors as well as the topology of its descendants in the GO graph. Secondly, WIS calculates the IC of a term set by means of considering the weighted inherited semantics of terms. Finally, WIS estimates the gene functional similarity based on the IC overlap ratio of term sets. WIS is superior to some other representative measures on the experiments of functional classification of genes in a biological pathway, collaborative evaluation of GO-based semantic similarity measures, protein-protein interaction prediction and correlation with gene expression. Further analysis suggests that WIS takes fully into account the specificity of terms and the weighted inherited semantics of terms between GO terms.
CONCLUSIONS: The proposed WIS method is an effective and reliable way to compare gene function. The web service of WIS is freely available at http://nclab.hit.edu.cn/WIS/ .

PMID: 28155727 [PubMed - in process]

Mobile Technology in the Perioperative Arena: Rapid Evolution and Future Disruption.

Anesth Analg. 2017 Feb 01;:

Authors: Rothman BS, Gupta RK, McEvoy MD

Abstract
Throughout the history of medicine, physicians have relied upon disruptive innovations and technologies to improve the quality of care delivered, patient outcomes, and patient satisfaction. The implementation of mobile technology in health care is quickly becoming the next disruptive technology. We first review the history of mobile technology over the past 3 decades, discuss the impact of hardware and software, explore the rapid expansion of applications (apps), and evaluate the adoption of mobile technology in health care. Next, we discuss how technology serves as the vehicle that can transform traditional didactic learning into one that adapts to the learning behavior of the student by using concepts such as the flipped classroom, just-in-time learning, social media, and Web 2.0/3.0. The focus in this modern education paradigm is shifting from teacher-centric to learner-centric, including providers and patients, and is being delivered as context-sensitive, or semantic, learning. Finally, we present the methods by which connected health systems via mobile devices increase information collection and analysis from patients in both clinical care and research environments. This enhanced patient and provider connection has demonstrated benefits including reducing unnecessary hospital readmissions, improved perioperative health maintenance coordination, and improved care in remote and underserved areas. A significant portion of the future of health care, and specifically perioperative medicine, revolves around mobile technology, nimble learners, patient-specific information and decision-making, and continuous connectivity between patients and health care systems. As such, an understanding of developing or evaluating mobile technology likely will be important for anesthesiologists, particularly with an ever-expanding scope of practice in perioperative medicine.

PMID: 28151816 [PubMed - as supplied by publisher]

Genes2GO: A web application for querying gene sets for specific GO terms.

Bioinformation. 2016;12(3):231-232

Authors: Chawla K, Kuiper M

Abstract
Gene ontology annotations have become an essential resource for biological interpretations of experimental findings. The process of gathering basic annotation information in tables that link gene sets with specific gene ontology terms can be cumbersome, in particular if it requires above average computer skills or bioinformatics expertise. We have therefore developed Genes2GO, an intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database. Genes2GO produces a binary matrix file, indicating for each gene the presence or absence of specific annotations for a gene. It should be noted that other GO tools do not offer this user-friendly access to annotations.
AVAILABILITY: Genes2GO is freely available and listed under http://www.semantic-systems-biology.org/tools/externaltools/.

PMID: 28149059 [PubMed]

SAFE: SPARQL Federation over RDF Data Cubes with Access Control.

J Biomed Semantics. 2017 Feb 01;8(1):5

Authors: Khan Y, Saleem M, Mehdi M, Hogan A, Mehmood Q, Rebholz-Schuhmann D, Sahay R

Abstract
BACKGROUND: Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data.
RESULTS: We present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE's indexing system does not hold any data instances-it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change.
CONCLUSIONS: We validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

PMID: 28148277 [PubMed - in process]

Toward cognitive pipelines of medical assistance algorithms.

Int J Comput Assist Radiol Surg. 2016 Sep;11(9):1743-53

Authors: Philipp P, Maleshkova M, Katic D, Weber C, Götz M, Rettinger A, Speidel S, Kämpgen B, Nolden M, Wekerle AL, Dillmann R, Kenngott H, Müller B, Studer R

Abstract
PURPOSE: Assistance algorithms for medical tasks have great potential to support physicians with their daily work. However, medicine is also one of the most demanding domains for computer-based support systems, since medical assistance tasks are complex and the practical experience of the physician is crucial. Recent developments in the area of cognitive computing appear to be well suited to tackle medicine as an application domain.
METHODS: We propose a system based on the idea of cognitive computing and consisting of auto-configurable medical assistance algorithms and their self-adapting combination. The system enables automatic execution of new algorithms, given they are made available as Medical Cognitive Apps and are registered in a central semantic repository. Learning components can be added to the system to optimize the results in the cases when numerous Medical Cognitive Apps are available for the same task. Our prototypical implementation is applied to the areas of surgical phase recognition based on sensor data and image progressing for tumor progression mappings.
RESULTS: Our results suggest that such assistance algorithms can be automatically configured in execution pipelines, candidate results can be automatically scored and combined, and the system can learn from experience. Furthermore, our evaluation shows that the Medical Cognitive Apps are providing the correct results as they did for local execution and run in a reasonable amount of time.
CONCLUSION: The proposed solution is applicable to a variety of medical use cases and effectively supports the automated and self-adaptive configuration of cognitive pipelines based on medical interpretation algorithms.

PMID: 26646415 [PubMed - indexed for MEDLINE]

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation.

PLoS One. 2017;12(1):e0169658

Authors: Audeh B, Beigbeder M, Zimmermann A, Jaillon P, Bousquet C

Abstract
The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites.

PMID: 28122056 [PubMed - in process]

Generalization and maintenance of treatment gains in primary progressive aphasia (PPA): a systematic review.

Int J Lang Commun Disord. 2017 Jan 24;:

Authors: Cadório I, Lousada M, Martins P, Figueiredo D

Abstract
BACKGROUND: Cognitive-linguistic treatments and interventions targeting communication have been developed within the context of primary progressive aphasia (PPA), however knowledge about the scope of generalization and maintenance of therapy gains considering PPA subtypes remains scarce and awaits systematic investigation.
AIMS: To analyse the effects of semantic therapy on generalization and maintenance of treatment outcomes in individuals with PPA, considering its different subtypes.
METHODS & PROCEDURES: Central, PubMed, Medline, Web of Knowledge and Scopus were used to retrieve articles of interest. A total of 25 non-randomized studies published between 2000 and 2016 met the eligibility criteria and therefore were included in this study.
MAIN CONTRIBUTION: This systematic review provides evidence-based information for clinical practice in PPA. Generalization and maintenance effects post-treatment for each PPA variant are analysed and discussed. Several factors are described as important to maximize the scope for generalization and maintenance of treatment gains.
CONCLUSIONS & IMPLICATIONS: Generalization is particularly hard to achieve in the semantic variant, as in the face of degraded semantic knowledge learning is rigid and context dependent. In contrast, non-fluent and logopenic variants offer better scope for generalization. Maintenance patterns do not seem to be influenced by PPA subtype, but rather by other factors such as continued practice, treatment length and frequency of sessions. In the future, clinicians should consider the PPA subtype when planning the treatment protocol.

PMID: 28120406 [PubMed - as supplied by publisher]