Detectors could spot plagiarism in research proposals

Having all been involved in proposal evaluation, we believe the studies indicate that a text matching analysis of research proposals could reduce plagiarism in subsequent publications. For instance, when European Commission evaluators have met in the past to evaluate research proposals, they received printed copies which had to be returned before the panel members left, and had no computer access during deliberations. A plagiarism detector using text-mining methods could be used instead of the current security measures. Such a system could, in principle, detect similarities to previous submissions and uncited sources using advanced document segmentation. Only official agencies have access to confidential proposals and the funds to experiment with automated plagiarism-detectors. It is important that they should investigate these approaches to reducing the possibility of scientific misconduct

An Ontology Based Method to Solve Query Identifier Heterogeneity in Post-Genomic Clinical Trials

The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains—e.g. clinical and genetic data. One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases. In this work, we describe an approach to overcome heterogeneities in identifiers inside queries. We present an ontology classifying the most common identifier semantic heterogeneities, and a service that makes use of it to cope with the problem using the described approach. Finally, we illustrate the solution by analysing a set of real queries

Web Services: Introduction and State of the Art

In this paper we provide a brief introduction to Web Services, including the main specifications: SOAP, WSDL and UDDI. We also describe other specifications that complement them and provide solutions to aspects needed to develop service oriented architectures based on Web Services. We also address some of the research issues open, including the semantic description of services, which is one of the issues to which more effort is being devoted currently. Finally, we list the main areas where Web Service technology is being applied successfully in the context of enterprises

Cohesion and Complex System Structure

In the self-organizing complex dynamical systems that form holarchies, the decisions (or reactions) of their components (constituents) sometimes are crucial because they may involve the proper existence of the system. Additionally, in the real world, these components are immersed in highly complex environments of which have an incomplete or inadequate knowledge and they can’t be completely consistent about their preferences and their beliefs, can show a bounded rationality, etc. All these circumstances affect the way in which the components not only behave, but also emerge and disappear. In this work the necessary and sufficient conditions previously given for the holons formation are reviewed in the light of these facts using for the uncertainty/randomness handling the fuzzy probabilities theory (thus modeling the decision making process through the fuzzy decision making under risk theory), and, from these conditions, the concept of holon cohesion is derived and introduced as a generalization of the reliability of a system

A Knowledge Engineering Approach to Recognizing and Extracting Sequences of Nucleic Acids from Scientific Literature

In this paper we present a knowledge engineering approach to automatically recognize and extract genetic sequences from scientific articles. To carry out this task, we use a preliminary recognizer based on a finite state machine to extract all candidate DNA/RNA sequences. The latter are then fed into a knowledge-based system that automatically discards false positives and refines noisy and incorrectly merged sequences. We created the knowledge base by manually analyzing different manuscripts containing genetic sequences. Our approach was evaluated using a test set of 211 full-text articles in PDF format containing 3134 genetic sequences. For such set, we achieved 87.76% precision and 97.70% recall respectively. This method can facilitate different research tasks. These include text mining, information extraction, and information retrieval research dealing with large collections of documents containing genetic sequences

Automatic Generation of Integration and Preprocessing Ontologies for Biomedical Sources in a Distributed Scenario

Access to a large number of remote data sources has boosted research in biomedicine, where different biological and clinical research projects are based on collaborative efforts among international organizations. In this scenario, the authors have developed various methods and tools in the area of database integration, using an ontological approach. This paper describes a method to automatically generate preprocessing structures (ontologies) within an ontology-based KDD model. These ontologies are obtained from the analysis of data sources, searching for: (i) valid numerical ranges (using clustering techniques), (ii) different scales, (iii) synonym transformations based on known dictionaries and (iv)typographical errors. To test the method, experiments were carried out with four biomedical databases―containing rheumatoid arthritis, gene expression patterns, biological processes and breast cancer patients― proving the performance of the approach. This method supports experts in data analysis processes, facilitating the detection of inconsistencies

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems

An Automatic Method for Retrieving and Indexing Catalogues of Biomedical Courses

Although there is wide information about Biomedical Informatics education and courses in different Websites, information is usually not exhaustive and difficult to update. We propose a new methodology based on information retrieval techniques for extracting, indexing and retrieving automatically information about educational offers. A web application has been developed to make available such information in an inventory of courses and educational offers

Cloud Computing Service for Managing Large Medical Image Data-Sets Using Balanced Collaborative Agents

Managing large medical image collections is an increasingly demanding important issue in many hospitals and other medical settings. A huge amount of this information is daily generated, which requires robust and agile systems. In this paper we present a distributed multi-agent system capable of managing very large medical image datasets. In this approach, agents extract low-level information from images and store them in a data structure implemented in a relational database. The data structure can also store semantic information related to images and particular regions. A distinctive aspect of our work is that a single image can be divided so that the resultant sub-images can be stored and managed separately by different agents to improve performance in data accessing and processing. The system also offers the possibility of applying some region-based operations and filters on images, facilitating image classification. These operations can be performed directly on data structures in the database

Nanoinformática: retos e iniciativas para la gestión de la información generada en la investigación nanomédica

Durante la última década la investigación en nanomedicina ha generado gran cantidad de datos, heterogéneos, distribuidos en múltiples fuentes de información. El uso de las Tecnologías de la Información y la Comunicación (TIC) puede facilitar la investigación médica a escala nanométrica, proporcionando mecanismos y herramientas que permitan gestionar todos esos datos de una manera inteligente. Mientras que la informática biomédica comprende el procesamiento y gestión de la información generada desde el nivel de salud pública y aplicación clínica hasta el nivel molecular, la nanoinformática extiende este ámbito para incluir el “nivel nano”, ocupándose de gestionar y analizar los resultados generados durante la investigación en nanomedicina y desarrollar nuevas líneas de trabajo en este espacio interdisciplinar. En esta nueva área científica, la nanoinformática (que podría consolidarse como una auténtica disciplina en los próximos años), elGrupo de Informática Biomédica (GIB) de la Universidad Politécnica de Madrid (UPM) participa en numerosas iniciativas, que se detallan a continuación