µ -ANT: semantic microaggregation-based anonymization tool.

MOTIVATION: Detailed patient data are crucial for medical research. Yet, these healthcare data can only be released for secondary use if they have undergone anonymization. RESULTS: We present and describe µ-ANT, a practical and easily configurable anonymization tool for (healthcare) data. It implements several state-of-the-art methods to offer robust privacy guarantees and preserve the utility of the anonymized data as much as possible. µ-ANT also supports the heterogenous attribute types commonly found in electronic healthcare records and targets both practitioners and software developers interested in data anonymization. AVAILABILITY AND IMPLEMENTATION: (source code, documentation, executable, sample datasets and use case examples) https://github.com/CrisesUrv/microaggregation-based_anonymization_tool.

Utility-preserving privacy protection of textual healthcare documents.

The adoption of ITs by medical organisations makes possible the compilation of large amounts of healthcare data, which are quite often needed to be released to third parties for research or business purposes. Many of this data are of sensitive nature, because they may include patient-related documents such as electronic healthcare records. In order to protect the privacy of individuals, several legislations on healthcare data management, which state the kind of information that should be protected, have been defined. Traditionally, to meet with current legislations, a manual redaction process is applied to patient-related documents in order to remove or black-out sensitive terms. This process is costly and time-consuming and has the undesired side effect of severely reducing the utility of the released content. Automatic methods available in the literature usually propose ad-hoc solutions that are limited to protect specific types of structured information (e.g. e-mail addresses, social security numbers, etc.); as a result, they are hardly applicable to the sensitive entities stated in current regulations that do not present those structural regularities (e.g. diseases, symptoms, treatments, etc.). To tackle these limitations, in this paper we propose an automatic sanitisation method for textual medical documents (e.g. electronic healthcare records) that is able to protect, regardless of their structure, sensitive entities (e.g. diseases) and also those semantically related terms (e.g. symptoms) that may disclose the former ones. Contrary to redaction schemes based on term removal, our approach improves the utility of the protected output by replacing sensitive terms with appropriate generalisations retrieved from several medical and general-purpose knowledge bases. Experiments conducted on highly sensitive documents and in coherency with current regulations on healthcare data privacy show promising results in terms of the practical privacy and utility of the protected output.

Enabling semantic similarity estimation across multiple ontologies: an evaluation in the biomedical domain.

The estimation of the semantic similarity between terms provides a valuable tool to enable the understanding of textual resources. Many semantic similarity computation paradigms have been proposed both as general-purpose solutions or framed in concrete fields such as biomedicine. In particular, ontology-based approaches have been very successful due to their efficiency, scalability, lack of constraints and thanks to the availability of large and consensus ontologies (like WordNet or those in the UMLS). These measures, however, are hampered by the fact that only one ontology is exploited and, hence, their recall depends on the ontological detail and coverage. In recent years, some authors have extended some of the existing methodologies to support multiple ontologies. The problem of integrating heterogeneous knowledge sources is tackled by means of simple terminological matchings between ontological concepts. In this paper, we aim to improve these methods by analysing the similarity between the modelled taxonomical knowledge and the structure of different ontologies. As a result, we are able to better discover the commonalities between different ontologies and hence, improve the accuracy of the similarity estimation. Two methods are proposed to tackle this task. They have been evaluated and compared with related works by means of several widely-used benchmarks of biomedical terms using two standard ontologies (WordNet and MeSH). Results show that our methods correlate better, compared to related works, with the similarity assessments provided by experts in biomedicine.

Semantic similarity estimation in the biomedical domain: an ontology-based information-theoretic perspective.

Semantic similarity estimation is an important component of analysing natural language resources like clinical records. Proper understanding of concept semantics allows for improved use and integration of heterogeneous clinical sources as well as higher information retrieval accuracy. Semantic similarity has been the focus of much research, which has led to the definition of heterogeneous measures using different theoretical principles and knowledge resources in a variety of contexts and application domains. In this paper, we study several of these measures, in addition to other similarity coefficients (not necessarily framed in a semantic context) that may be useful in determining the similarity of sets of terms. In order to make them easier to interpret and improve their applicability and accuracy, we propose a framework grounded in information theory that allows the measures studied to be uniformly redefined. Our framework is based on approximating concept semantics in terms of Information Content (IC). We also propose computing IC in a scalable and efficient manner from the taxonomical knowledge modelled in biomedical ontologies. As a result, new semantic similarity measures expressed in terms of concept Information Content are presented. These measures are evaluated and compared to related works using a benchmark of medical terms and a standard biomedical ontology. We found that an information-theoretical redefinition of well-known semantic measures and similarity coefficients, and an intrinsic estimation of concept IC result in noticeable improvements in their accuracy.

An ontology-based measure to compute semantic similarity in biomedicine.

Proper understanding of textual data requires the exploitation and integration of unstructured and heterogeneous clinical sources, healthcare records or scientific literature, which are fundamental aspects in clinical and translational research. The determination of semantic similarity between word pairs is an important component of text understanding that enables the processing, classification and structuring of textual resources. In the past, several approaches for assessing word similarity by exploiting different knowledge sources (ontologies, thesauri, domain corpora, etc.) have been proposed. Some of these measures have been adapted to the biomedical field by incorporating domain information extracted from clinical data or from medical ontologies (such as MeSH or SNOMED CT). In this paper, these approaches are introduced and analyzed in order to determine their advantages and limitations with respect to the considered knowledge bases. After that, a new measure based on the exploitation of the taxonomical structure of a biomedical ontology is proposed. Using SNOMED CT as the input ontology, the accuracy of our proposal is evaluated and compared against other approaches according to a standard benchmark of manually ranked medical terms. The correlation between the results of the evaluated measures and the human experts' ratings shows that our proposal outperforms most of the previous measures avoiding, at the same time, some of their limitations.

Using ontologies for structuring organizational knowledge in Home Care assistance.

PURPOSE: Information Technologies and Knowledge-based Systems can significantly improve the management of complex distributed health systems, where supporting multidisciplinarity is crucial and communication and synchronization between the different professionals and tasks becomes essential. This work proposes the use of the ontological paradigm to describe the organizational knowledge of such complex healthcare institutions as a basis to support their management. The ontology engineering process is detailed, as well as the way to maintain the ontology updated in front of changes. The paper also analyzes how such an ontology can be exploited in a real healthcare application and the role of the ontology in the customization of the system. The particular case of senior Home Care assistance is addressed, as this is a highly distributed field as well as a strategic goal in an ageing Europe. MATERIALS AND METHODS: The proposed ontology design is based on a Home Care medical model defined by an European consortium of Home Care professionals, framed in the scope of the K4Care European project (FP6). Due to the complexity of the model and the knowledge gap existing between the - textual - medical model and the strict formalization of an ontology, an ontology engineering methodology (On-To-Knowledge) has been followed. RESULTS: After applying the On-To-Knowledge steps, the following results were obtained: the feasibility study concluded that the ontological paradigm and the expressiveness of modern ontology languages were enough to describe the required medical knowledge; after the kick-off and refinement stages, a complete and non-ambiguous definition of the Home Care model, including its main components and interrelations, was obtained; the formalization stage expressed HC medical entities in the form of ontological classes, which are interrelated by means of hierarchies, properties and semantically rich class restrictions; the evaluation, carried out by exploiting the ontology into a knowledge-driven e-health application running on a real scenario, showed that the ontology design and its exploitation brought several benefits with regards to flexibility, adaptability and work efficiency from the end-user point of view; for the maintenance stage, two software tools are presented, aimed to address the incorporation and modification of healthcare units and the personalization of ontological profiles. CONCLUSIONS: The paper shows that the ontological paradigm and the expressiveness of modern ontology languages can be exploited not only to represent terminology in a non-ambiguous way, but also to formalize the interrelations and organizational structures involved in a real and distributed healthcare environment. This kind of ontologies facilitates the adaptation in front of changes in the healthcare organization or Care Units, supports the creation of profile-based interaction models in a transparent and seamless way, and increases the reusability and generality of the developed software components. As a conclusion of the exploitation of the developed ontology in a real medical scenario, we can say that an ontology formalizing organizational interrelations is a key component for building effective distributed knowledge-driven e-health systems.