Ana Jimenez-Castellanos

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

BackgroundOver 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.ResultsWe 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.ConclusionsCDAPubMed 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.

Accessing advanced computational resources in Africa through Cloud Computing

Low resources in many African locations do not allow many African scientists and physicians to access the latest advances in technology. This deficiency hinders the daily life of African professionals that often cannot afford, for instance, the cost of internet fees or software licenses. The AFRICA BUILD project, funded by the European Commission and formed by four European and four African institutions, intends to provide advanced computational tools to African institutions in order to solve current technological limitations. In the context of AFRICA BUILD we have carried out, a series of experiments to test the feasibility of using Cloud Computing technologies in two different locations in Africa: Egypt and Burundi. The project aims to create a virtual platform to provide access to a wide range of biomedical informatics and learning resources to professionals and researchers in Africa.

Biomedical Literature Retrieval Based on Patient Information

Information and Communication Technologies has led to a biomedical data explosion. A proportional growth has been produced regarding the amount of scientific literature, but information retrieval methods did not follow the same pattern. By using specialized clinical search engines such as PubMed, Medscape and Cochrane, biomedical publications has became instantly available for clinical users. However, additional parameters, such as user context, are not taken into account yet. Initial queries still retrieve too many results without a relevance-based ranking. The objective of this work was to develop a new method to enhance scientific literature searches from various sources, by including patient information in the retrieval process. Two pathologies have been used to test the proposed method: diabetes and arterial hypertension. Results obtained suggest the suitability of the approach, highlighting the publications related to patient characteristics.

Identifying gaps in health research and training in Africa: Designing online surveys for Cloud-oriented training

Education and research are two fundamental pillars to ensure progress. Without an appropriate education, quality research is not feasible. In the case of developing countries, these issues become more challenging since literacy and access to information are still unsolved. In this regard, numerous initiatives around the world have been launched for promoting education by applying Information and Communication Technologies (ICT). However, introducing such technologies without considering the actual needs and idiosyncratic issues of target countries usually leads to failure since problems are different in developed countries than in developing ones. In this paper we present the studies carried out within the framework of the AFRICA BUILD project aimed to identify how Cloud computing technologies might contribute to alleviate the existing educational and training gaps in health research in Africa.

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

A Cloud Computing Service for managing biomedical image collections

A huge quantity of biomedical images is generated every day. Building effective and agile systems for managing these collections has become an important and expensive issue for hospitals and institutions. In this paper we present a cloud computing service and its application for the storage and analysis of large image collections, specifically for very-large images. This Cloud Computing Service allows users to manage image collections in a relatively low-cost manner. The service is internally implemented by a balanced multiagent system. A novel aspect of the system is that one image could be divided in several, and those can then be stored and managed separately. This feature improves performance in data processing and information retrieval.