Elena Cardillo

A collaborative semantic web layer to enhance legacy systems

This paper introduces a framework to add a semantic web layer to legacy organizational information, and describes its application to the use case provided by the Italian National Research Council (CNR) intraweb. Building on a traditional web-based view of information from different legacy databases, we have performed a semantic porting of data into a knowledge base, dependent on an OWL domain ontology. We have enriched the knowledge base by means of text mining techniques, in order to discover on-topic relations. Several reasoning techniques have been applied, in order to infer relevant implicit relationships. Finally, the ontology and the knowledge base have been deployed on a semantic wiki by means of the WikiFactory tool, which allows users to browse the ontology and the knowledge base, to introduce new relations, to revise wrong assertions in a collaborative way, and to perform semantic queries. In our experiments, we have been able to easily implement several functionalities, such as expert finding, by simply formulating ad-hoc queries from either an ontology editor or the semantic wiki interface. The result is an intelligent and collaborative front end, which allow users to add information, fill gaps, or revise existing information on a semantic basis, while keeping the knowledge base automatically updated.

Logical Analysis of Mappings between Medical Classification Systems

Medical classification systems provide an essential instrument for unambiguously labeling clinical concepts in processes and services in healthcare and for improving the accessibility and elaboration of the medical content in clinical information systems. Over the last two decades the standardization efforts have established a number of classification systems as well as conversion mappings between them. Although these mappings represent the agreement reached between human specialists who devised them, there is no explicit formal reference establishing the precise meaning of the mappings. In this work we close this semantic gap by applying the results that have been recently reached in the area of AI and the Semantic Web on the formalization and analysis of mappings between heterogeneous conceptualizations. Practically, we focus on two classification systems which have received great widespread and preference within the European Union, namely ICPC-2 (International Classification of Primary Care) and ICD-10 (International Classification of Diseases). The particular contributions of this work are: the logical encoding in OWL of ICPC-2 and ICD-10 classifications; the formalization of the existing ICPC-ICD conversion mappings in terms of OWL axioms and further verification of its coherence using the logical reasoning; and finally, the outline of the other semantic techniques for automated analysis of implications of future mapping changes between ICPC and ICD classifications.

A Methodology for Knowledge Acquisition in Consumer-Oriented Healthcare

In Consumer-oriented Healthcare Informatics it is still difficult for laypersons to find, understand, and act on health information. This is due to the communication gap between specialized medical terminology used by healthcare professionals and “lay” medical terminology used by healthcare consumers. So there is a need to create consumer-friendly terminologies reflecting the different ways consumers and patients express and think about health topics. An additional need is to map these terminologies with existing clinically-oriented terminologies. This work suggests a methodology to acquire consumer health terminology for creating a Consumer-oriented Medical Vocabulary for Italian that mitigates this gap. This resource could be used in Personal Health Records to improve users’ accessibility to their healthcare data. In order to evaluate this methodology we mapped “lay” terms with standard specialized terminologies to find overlaps. Results showed that our approach provided many “lay” terms that can be considered good synonyms for medical concepts.

Process Fragment Recognition in Clinical Documents

We describe a first experiment on automated activity and relation identification, and more in general, on the automated identification and extraction of computer-interpretable guideline fragments from clinical documents. We rely on clinical entity and relation (activities, actors, artifacts and their relations) recognition techniques and use MetaMap and the UMLS Metathesaurus to provide lexical information. In particular, we study the impact of clinical document syntax and semantics on the precision of activity and temporal relation recognition.

Assessing ICD-9-CM and ICPC-2 Use in Primary Care. An Italian Case Study

Controlled vocabularies and standardized coding systems play a fundamental role in the healthcare domain. The International Classification of Diseases (ICD) is one of the most widely used classification systems for clinical problems and procedures. In Italy the 9th revision of the standard is used and recommended in primary care for encoding prescription documents. This paper describes a statistical and terminological study to assess ICD-9-CM use in primary care and its comparison to the International Classification of Primary Care (ICPC), specifically designed for primary care. The study has been conducted by analyzing the clinical records of about 199,000 patients provided by a set of 166 General Practitioners (GPs) in different Italian areas. The analysis has been based on several techniques for detecting coding practice and errors, like natural language processing and text-similarity comparison. Results showed that the selected GPs do not fully exploit the diseases and procedures descriptive capabilities of ICD-9-CM due to its complexity. Furthermore, compared to ICPC-2, it resulted less feasible in the primary care setting, particularly for the high granularity of the structure and for the lack of reasons for encounters.

On the Collaborative Development of Application Ontologies: A Practical Case Study with a SME

With semantic technologies coming of age, ontology-based applications are becoming more prevalent. These applications exploit the content encoded in ontologies to perform different tasks and operations. The development of ontologies to be used by a specific application presents some peculiarities compared to the modelling process of other types of ontologies. These peculiarities are related to the choice of the ontology metamodel which should be optimised for the application, and the possibility of an indirect evaluation of the ontology by running the application. In this paper we report the experience of collaboratively building an ontology for an application that supports the development of Individual Educational Plans (IEPs) for pupils with special needs. This application is a commercial product of a Small-Medium Enterprise (SME). The ontology is the result of a one-year long modelling experience that involved more than a dozen users having different expertise and competences, such as educationalists, psychologists, teachers, knowledge engineers, and application engineers. Beside describing the modelling process and tool, we report the lessons learned in collaboratively modelling an application ontology in a very concrete case. We believe our experience is worth reporting as our findings and lessons learned may be beneficial for similar modelling initiatives regarding the development of application ontologies.

Mapping French terms in a Belgian guideline on heart failure to international classifications and nomenclatures: the devil is in the detail

INTRODUCTION With growing sophistication of eHealth platforms, medical information is increasingly shared across patients, health care providers, institutions and across borders. This implies more stringent demands on the quality of data entry at the point-of-care. Non-native English-speaking general practitioners (GPs) experience difficulties in interacting with international classification systems and nomenclatures to facilitate the secondary use of their data and to ensure semantic interoperability. AIM To identify words and phrases pertaining to the heart failure domain and to explore the difficulties in mapping to corresponding concepts in ICPC-2, ICD-10, SNOMED-CT and UMLS. METHODS The medical concepts in a Belgian guideline for GPs in its French version were extracted manually and coded first in ICPC-2, then ICD-10 by a physician, an expert in classification systems. In addition, mappings were sought with SNOMED-CT and UMLS concepts, using the UMLS SNOMED-CT browser. RESULTS We identified 143 words and phrases, of which 128 referred to a single concept (1-to-1 mapping), while 15 referred to two or more concepts (1-to-n mapping to ICPC rubrics or to the other nomenclatures). In the guideline, words or phrases were often too general for specific mapping to a code or term. Marked discrepancy between semantic tags and types was found. CONCLUSION This article shows the variability of the various international classifications and nomenclatures, the need for structured guidelines with more attention to precise wording and the need for classification expertise embedded in sophisticated terminological resources. End users need support to perform their clinical work in their own language, while still assuring standardised and semantic interoperable medical registration. Collaboration between computational linguists, knowledge engineers, health informaticians and domain experts is needed.

A Lexical-Ontological Resource for Consumer Heathcare

In Consumer Healthcare Informatics it is still difficult for laypersons to understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and Semantic Web technologies. The system is based on the development of a consumer-oriented medical terminology which will be integrated with other existing domain ontologies/terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems by providing many knowledge services to help users in accessing and managing their healthcare data.

Development, dissemination, and applications of a new terminological resource the Q-Code taxonomy for professional aspects of General Practice / Family Medicine.

Abstract Background: While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. Objectives: To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. Development: The Q-Codes taxonomy was developed from Lamberts’ seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) (http://www.hetop.eu/Q). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. Applications: This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.

A Lexical-Ontological Resource for Consumer Healthcare

In Consumer Healthcare Informatics it is still difficult for laypeople to find, understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and semantic web technologies. The system is based on the development of a consumer-oriented medical terminology that will be integrated with other medical domain ontologies and terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems, such as Personal Health Records, by providing many knowledge services to help users in accessing and managing their healthcare data.