Understanding research dynamics

Rexplore leverages novel solutions in data mining, semantic technologies and visual analytics, and provides an innovative environment for exploring and making sense of scholarly data. Rexplore allows users: 1) to detect and make sense of important trends in research; 2) to identify a variety of interesting relations between researchers, beyond the standard co-authorship relations provided by most other systems; 3) to perform fine-grained expert search with respect to detailed multi-dimensional parameters; 4) to detect and characterize the dynamics of interesting communities of researchers, identified on the basis of shared research interests and scientific trajectories; 5) to analyse research performance at different levels of abstraction, including individual researchers, organizations, countries, and research communities

Exploring scholarly data with Rexplore.

Despite the large number and variety of tools and services available today for exploring scholarly data, current support is still very limited in the context of sensemaking tasks, which go beyond standard search and ranking of authors and publications, and focus instead on i) understanding the dynamics of research areas, ii) relating authors ‘semantically’ (e.g., in terms of common interests or shared academic trajectories), or iii) performing fine-grained academic expert search along multiple dimensions. To address this gap we have developed a novel tool, Rexplore, which integrates statistical analysis, semantic technologies, and visual analytics to provide effective support for exploring and making sense of scholarly data. Here, we describe the main innovative elements of the tool and we present the results from a task-centric empirical evaluation, which shows that Rexplore is highly effective at providing support for the aforementioned sensemaking tasks. In addition, these results are robust both with respect to the background of the users (i.e., expert analysts vs. ‘ordinary’ users) and also with respect to whether the tasks are selected by the evaluators or proposed by the users themselves

Design issues for agent-based resource locator systems

While knowledge is viewed by many as an asset, it is often difficult to locate particularitems within a large electronic corpus. This paper presents an agent based framework for the location of resources to resolve a specific query, and considers the associated design issue. Aspects of the work presented complements current research into both expertise finders and recommender systems. The essential issues for the proposed design are scalability, together ith the ability to learn and adapt to changing resources. As knowledge is often implicit within electronic resources, and therefore difficult to locate, we have proposed the use of ontologies, to extract the semantics and infer meaning to obtain the results required. We explore the use of communities of practice, applying ontology-based networks, and e-mail message exchanges to aid the resource discovery process

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Towards personalization in digital libraries through ontologies

In this paper we describe a browsing and searching personalization system for digital libraries based on the use of ontologies for describing the relationships between all the elements which take part in a digital library scenario of use. The main goal of this project is to help the users of a digital library to improve their experience of use by means of two complementary strategies: first, by maintaining a complete history record of his or her browsing and searching activities, which is part of a navigational user profile which includes preferences and all the aspects related to community involvement; and second, by reusing all the knowledge which has been extracted from previous usage from other users with similar profiles. This can be accomplished in terms of narrowing and focusing the search results and browsing options through the use of a recommendation system which organizes such results in the most appropriate manner, using ontologies and concepts drawn from the semantic web field. The complete integration of the experience of use of a digital library in the learning process is also pursued. Both the usage and information organization can be also exploited to extract useful knowledge from the way users interact with a digital library, knowledge that can be used to improve several design aspects of the library, ranging from internal organization aspects to human factors and user interfaces. Although this project is still on an early development stage, it is possible to identify all the desired functionalities and requirements that are necessary to fully integrate the use of a digital library in an e-learning environment

Semantic Filtering of Scientific Articles guided by a Domain Ontology

International audienceThe problem that we address in this paper is how to improve the accuracy of retrieving specialized information within a textual scientific corpus. We present a new approach in which the keywords expressing the bibliographical needs of a researcher are related to a domain ontology. We illustrate how such a declarative ontolology-based approach can be used both for computing varied statistics, and also for helping experts to find useful fine-grained information within a textual corpus