p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data

Secure access to patient data is becoming of increasing importance, as medical informatics grows in significance, to both assist with population health studies, and patient specific medicine in support of treatment. However, assembling the many different types of data emanating from the clinic is in itself a difficulty, and doing so across national borders compounds the problem. In this paper we present our solution: an easy to use distributed informatics platform embedding a state of the art data warehouse incorporating a secure pseudonymisation system protecting access to personal healthcare data. Using this system, a whole range of patient derived data, from genomics to imaging to clinical records, can be assembled and linked, and then connected with analytics tools that help us to understand the data. Research performed in this environment will have immediate clinical impact for personalised patient healthcare.

Toward a view-oriented approach for aligning RDF-based biomedical repositories

INTRODUCTION

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

BACKGROUND

The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information.

OBJECTIVES

To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches.

METHODS

Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches.

RESULTS

We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema.

CONCLUSIONS

The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.

[Temporal evolution of tuberculosis and human immunodeficiency virus infection in a population cared for in a hospital in Málaga]

BACKGROUND

We have studied the incidence of tuberculosis++ disease, HIV infection and their association during a period of 6 years using samples analysed in a third level hospital laboratory.

MATERIAL AND METHOD

21,242 samples for mycobacteria and 63,425 for HIV antibodies were analysed between 1993 and 1998. The protocol used for mycobacteria consisted of Lowenstein-Jensen, hemoculture, biochemical tests for identification and DNA probe. The diagnosis of HIV was performed using screening with mix EIA HIV 1 + 2, confirmed with Western-blot. Spearman coefficient correlation was used for study of tendency.

RESULTS

1,613 samples (7.5%) positive for mycobacteria from 566 patients (98 females and 428 males) aging between 31 and 40 years (46.9%) were detected. The highest incidence for tuberculosis was observed in 1995 (49.2 x 10(5) and was followed by a decreasing linear tendency. Mycobacterium tuberculosis (96%) and M. bovis (2.7%) were most frequent agents. 2,295 samples (3.6%) showed anti-HIV (406 females and 1,889 males). 54.1% of the infected patients belonged to the age interval 21 to 40 years. The highest incidence was observed in 1994 and was followed by a significant decrease (p < 0.05). The percentage of patients co-infected with tuberculosis-HIV was 39.7% with a maximum in 1995 followed by a linear decrease.

CONCLUSIONS

The incidence of both infections and co-infection was very high in the first triennium and was followed by a progressive decrease. The decrease of HIV preceded tuberculosis. The result suggest a possible epidemiological correlation between both infections.

Metabolic acidosis and coma due to an overdose of nalidixic acid

A case of severe metabolic acidosis and coma after taking 28 g of nalidixic acid is described. After administration of 600 mEq of sodium bicarbonate the patient developed a respiratory alkalosis with secondary tetany. She recovered her state of consciousness nine hours later and the acid-base disturbance resolved after sixty hours.

[Acute abdomen due to hemoperitoneum as the first manifestation of a liver tumor. Report of four cases (author's transl)]

Four cases of spontaneous acute hemoperitoneum due to rupture of a liver tumor are presented. The resulting acute abdomen was the first manifestation of the neoplasia. The four tumors corresponded histopathologically to a cavernous hemangioma, a bening adenoma related to anabolizing androgens, and two hepatocarcinomas in cirrhotic livers. All of the patients presented abdominal pain and shock, the characteristics of which are described in this report. One of the patients died due to cardiac arrest before surgical treatment. Emergency surgery was performed on the other three, consisting of left hepatic lobectomy and ligature of the hepatic artery for the hemengioma, and segmented hepatectomy for the adenoma and the hepatocarcinoma. Only the patient with benign tumor survived. Lastly, the authors review the literature, commenting on the clinical, physiopathologic, therapeutic, and prognostic aspects.