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Dans les systèmes de recherche d'information, une indexation à base de termes et une correspondance à base d'intersection introduisent le problème de la disparité à cause des variations linguistiques. Avec l'objectif de résoudre ce problème, notre travail de thèse se positionne dans l'utilisation des ressources externes dans la recherche d'information. Ces ressources offrent non seulement les concepts pour une indexation plus précise et indépendante de langue, mais aussi une base de relations sémantiques entre ces concepts. Nous étudions en premier une indexation par concepts extraits à partir d'une ressource externe. Nous proposons ensuite de prendre en compte ces relations sémantiques entre les concepts dans la correspondance par un modèle de recherche d'information basé sur un réseau Bayésien des concepts et leurs relations sémantiques. Ainsi, nous étudions les extensions de l'indexation conceptuelle à des documents et requête structurés et multi-médias. Les fonctions de reclassement et de combinaison ont été proposées afin d'améliorer la performance de la recherche dans ces contextes. La validation des propositions est effectuée par des expérimentations dans la recherche d'information multilingue médicale, avec l'utilisation du méta thésaurus UMLS comme ressource externe.

The Unified Medical Language System Semantic Network (UMLS SN) being an upper-level abstraction of the biomedical domain has a complex structure due to many relationships, making it difficult for human orientation. Therefore, while the SN is a valuable source for modeling contents of the biomedical domain its usage is limited. NetON was designed and built for the automatic transformation of UMLS SN to OWL sublanguages to support semantic operations between biomedical systems. NetON uses advances in the Semantic Web, a candidate technology for sustaining knowledge intensive tasks. Ontology Web Language (OWL) sublanguage rules are used to represent information in UMLS SN. The major contribution of NetON is the opportunity of automatic transformation of UMLS SN to OWL sublanguages named as OWL Basic Species. The aim of NetON is maximum possible information transformation from UMLS SN. The only information that is not able to be transformed to any OWL Basic Species due to the lack of appropriate constructors in OWL standard is inheritance blockings in UMLS SN. In UMLS SN, there are unseen assertions that can be inferred by using inference rules on explicitly specified assertions which are not essentially valid for all the descendants. Deduction outcomes of any OWL reasoners on NetON OWL Basic Species will also include false positives due to the lack of inheritance blocking information. The algorithms of the second dimension consider the inheritance blocking information while executing inference rules. As this cannot be done by any OWL reasoner, the second dimension offers a solution for application developers.

One of the challenges in medical information retrieval is the terminology gap between the documents (commonly written by medical professional, using medical jargons), and the queries (commonly composed by non professional, using layman terms). In this thesis, we investigate the effect of query expansion, using domain-specific knowledge resource, to deal with this challenge. We use the Unified Medical Language System (UMLS), a repository of biomedical vocabularies, and utilize two of its resources: the Metathesaurus and the Semantic Network. We use the query set and document set provided by CLEF eHealth organizer. The query sets, provided for the medical information retrieval shared task, represent two different use cases of medical information retrieval. We experiment with query expansion using synonymous terms and non-synonymous concepts, blind relevance feedback, field weighting, and linear interpolation of different systems. Powered by TCPDF (www.tcpdf.org)

La combinaison du traitement sémantique des connaissances (Semantic Processing of Knowledge) et de la modélisation des étapes de raisonnement (Modeling Steps of Reasoning), utilisés dans le domaine clinique, offrent des possibilités intéressantes, nécessaires aussi, pour l’élaboration des ontologies médicales, utiles à l'exercice de cette profession. Dans ce cadre, l'interrogation de banques de données médicales multiples, comme MEDLINE, PubMed… constitue un outil précieux mais insuffisant car elle ne permet pas d'acquérir des connaissances facilement utilisables lors d’une démarche clinique. En effet, l'abondance de citations inappropriées constitue du bruit et requiert un tri fastidieux, incompatible avec une pratique efficace de la médecine.Dans un processus itératif, l'objectif est de construire, de façon aussi automatisée possible, des bases de connaissances médicales réutilisables, fondées sur des ontologies et, dans cette thèse, nous développons une série d'outils d'acquisition de connaissances qui combinent des opérateurs d'analyse linguistique et de modélisation de la clinique, fondés sur une typologie des connaissances mises en œuvre, et sur une implémentation des différents modes de raisonnement employés. La connaissance ne se résume pas à des informations issues de bases de données ; elle s’organise grâce à des opérateurs cognitifs de raisonnement qui permettent de la rendre opérationnelle dans le contexte intéressant le praticien.Un système multi-agents d’aide à la décision clinique (SMAAD) permettra la coopération et l'intégration des différents modules entrant dans l'élaboration d'une ontologie médicale et les sources de données sont les banques médicales, comme MEDLINE, et des citations extraites par PubMed ; les concepts et le vocabulaire proviennent de l'Unified Medical Language System (UMLS).Concernant le champ des bases de connaissances produites, la recherche concerne l'ensemble de la démarche clinique : le diagnostic, le pronostic, le traitement, le suivi thérapeutique de différentes pathologies, dans un domaine médical donné.Différentes approches et travaux sont recensés, dans l’état de question, et divers paradigmes sont explorés : 1) l'Evidence Base Medicine (une médecine fondée sur des indices). Un indice peut se définir comme un signe lié à son mode de mise en œuvre ; 2) Le raisonnement à partir de cas (RàPC) se fonde sur l'analogie de situations cliniques déjà rencontrées ; 3) Différentes approches sémantiques permettent d'implémenter les ontologies.Sur l’ensemble, nous avons travaillé les aspects logiques liés aux opérateurs cognitifs de raisonnement utilisés et nous avons organisé la coopération et l'intégration des connaissances exploitées durant les différentes étapes du processus clinique (diagnostic, pronostic, traitement, suivi thérapeutique). Cette intégration s’appuie sur un SMAAD : système multi-agent d'aide à la décision. / The combination of semantic processing of knowledge and modelling steps of reasoning employed in the clinical field offers exciting and necessary opportunities to develop ontologies relevant to the practice of medicine. In this context, multiple medical databases such as MEDLINE, PubMed are valuable tools but not sufficient because they cannot acquire the usable knowledge easily in a clinical approach. Indeed, abundance of inappropriate quotations constitutes the noise and requires a tedious sort incompatible with the practice of medicine.In an iterative process, the objective is to build an approach as automated as possible, the reusable medical knowledge bases is founded on an ontology of the concerned fields. In this thesis, the author will develop a series of tools for knowledge acquisition combining the linguistic analysis operators and clinical modelling based on the implemented knowledge typology and an implementation of different forms of employed reasoning. Knowledge is not limited to the information from data, but also and especially on the cognitive operators of reasoning for making them operational in the context relevant to the practitioner.A multi-agent system enables the integration and cooperation of the various modules used in the development of a medical ontology.The data sources are from medical databases such as MEDLINE, the citations retrieved by PubMed, and the concepts and vocabulary from the Unified Medical Language System (UMLS).Regarding the scope of produced knowledge bases, the research concerns the entire clinical process: diagnosis, prognosis, treatment, and therapeutic monitoring of various diseases in a given medical field.It is essential to identify the different approaches and the works already done.Different paradigms will be explored: 1) Evidence Based Medicine. An index can be defined as a sign related to its mode of implementation; 2) Case-based reasoning, which based on the analogy of clinical situations already encountered; 3) The different semantic approaches which are used to implement ontologies.On the whole, we worked on logical aspects related to cognitive operators of used reasoning, and we organized the cooperation and integration of exploited knowledge during the various stages of the clinical process (diagnosis, prognosis, treatment, therapeutic monitoring). This integration is based on a SMAAD: multi-agent system for decision support.

Cette thèse porte sur l’impact de l’usage de la sémantique dans le processus de la classification supervisée de textes. Cet impact est évalué au travers d’une étude expérimentale sur des documents issus du domaine médical et en utilisant UMLS (Unified Medical Language System) en tant que ressource sémantique. Cette évaluation est faite selon quatre scénarii expérimentaux d’ajout de sémantique à plusieurs niveaux du processus de classification. Le premier scénario correspond à la conceptualisation où le texte est enrichi avant indexation par des concepts correspondant dans UMLS ; le deuxième et le troisième scénario concernent l’enrichissement des vecteurs représentant les textes après indexation dans un sac de concepts (BOC – bag of concepts) par des concepts similaires. Enfin le dernier scénario utilise la sémantique au niveau de la prédiction des classes, où les concepts ainsi que les relations entre eux, sont impliqués dans la prise de décision. Le premier scénario est testé en utilisant trois des méthodes de classification: Rocchio, NB et SVM. Les trois autres scénarii sont uniquement testés en utilisant Rocchio qui est le mieux à même d’accueillir les modifications nécessaires. Au travers de ces différentes expérimentations nous avons tout d’abord montré que des améliorations significatives pouvaient être obtenues avec la conceptualisation du texte avant l’indexation. Ensuite, à partir de représentations vectorielles conceptualisées, nous avons constaté des améliorations plus modérées avec d’une part l’enrichissement sémantique de cette représentation vectorielle après indexation, et d’autre part l’usage de mesures de similarité sémantique en prédiction. / The main interest of this research is the effect of using semantics in the process of supervised text classification. This effect is evaluated through an experimental study on documents related to the medical domain using the UMLS (Unified Medical Language System) as a semantic resource. This evaluation follows four scenarios involving semantics at different steps of the classification process: the first scenario incorporates the conceptualization step where text is enriched with corresponding concepts from UMLS; both the second and the third scenarios concern enriching vectors that represent text as Bag of Concepts (BOC) with similar concepts; the last scenario considers using semantics during class prediction, where concepts as well as the relations between them are involved in decision making. We test the first scenario using three popular classification techniques: Rocchio, NB and SVM. We choose Rocchio for the other scenarios for its extendibility with semantics. According to experiment, results demonstrated significant improvement in classification performance using conceptualization before indexing. Moderate improvements are reported using conceptualized text representation with semantic enrichment after indexing or with semantic text-to-text semantic similarity measures for prediction.

Os sistemas de informação hospitalares geram diariamente uma quantidade significativa de dados em formato de texto livre, principalmente através de laudos médicos. Os laudos geralmente são recuperados do sistema através de informações associadas, como identificação do paciente, por datas ou profissional responsável. A recuperação da informação a partir do conteúdo descritivo é uma tarefa não trivial, pois os sistemas hospitalares em geral não são capazes de verificar o conteúdo de um texto livre em uma busca. Não havendo uma estrutura básica de organização, categorização ou indexação do texto livre armazenado nas bases hospitalares, uma grande quantidade de informação deixa de estar disponível para profissionais que necessitam delas, pois não sabem como recuperá-las. A capacidade de recuperação do conhecimento armazenado nestas bases de dados seria de grande valia para pesquisadores, estudantes ou mesmo para o estudo de casos clínicos. Segundo o contexto descrito, este trabalho propõe a criação de uma ferramenta de documentação automática que tem por objetivo gerar uma formatação associada ao texto livre de laudos em radiologia através da adição de informações obtidas a partir de sistemas de terminologias médicos padronizados. Com este procedimento, pretende-se facilitar a pesquisa pelo conhecimento armazenado em uma base de dados médicos através da informação adicional gerada. Para tanto o trabalho envolve pesquisas nas áreas de Ontologias e Extração deInformação, uma subárea do Processamento de linguagem Natural. As ontologias são importantes neste trabalho por tratarem o problema da padronização das terminologias usadas na escrita dos laudos, bem como para fornecer a organização e formatação necessária para que os laudos passem a ser partes de uma base de conhecimento. ) A Extração de Informação fornece os algoritmos e técnicas necessárias para que os laudos sejam documentados de forma automática, minimizando a necessidade de intervenção humana, normalmente muito custosa em termos de trabalho manual e tempo. Como resultado final obteve-se um conjunto de metodologias e ferramentas capazes de receber um laudo em texto livre e gerar um documento XML rotulado com códigos de conceitos definidos em um sistema de terminologias médico, como o UMLS ou o Radlex. Em todas as fases de processamento, até a obtenção do arquivo XML de saída, obteve-se valores de precisão superiores a 70%, um resultado bastante satisfatório se considerado que os algoritmos de PLN utilizados são todos baseados em regras. Em adição às ferramentas de PLN desenvolvidas, cita-se como resultados, os trabalhos desenvolvidos para avaliação de ontologias médicas segundo uma área médica prédefinido, a organização das ontologias em um formato útil para a utilização por algoritmos de PLN, a criação de um Corpus de laudos de Raio-X de Tórax em português para treinamento e testes de aplicações de PLN e um modelo de informação para documentação dos laudos. / Hospital Information Systems generate each day a significant amount of data in free text format, mainly as medical reports. Normally the reports are recovered from the system through associated information like patient identification, dates or responsible identification, for example. To recover a report by its content is not a trivial task since hospital systems are not capable of searching the free text content. Without a basic organizational structure, some categorization and indexing the free text stored on the hospital database is not accessible, since it cannot be recovered in the right context when it is needed. The ability of recovering the knowledge stored on these databases would be valuable for researchers, students or for the study of clinical cases. According to the described context, this work considers the creation of a tool for automatic documentation of medical reports written in free text. The main objective is to format radiological reports to achieve a more efficient way of recovering the knowledge stored in medical report\'s databases. To achieve this goal, information from medical terminology systems is added to the original report automatically. Such task requires some research in the field of Ontologies and Information Extraction, a sub field of Natural Language Processing. Ontologies are important in this work because they provide the standardization needed for the terminologies used in the written reports. It is important too forsupplying the organization necessary to format the reports in an adequate way to be stored on the knowledge base. Information Extraction supplies the algorithms and the necessary techniques to register in an automatic way the radiological reports, minimizing the human intervention, normally with a high cost in terms of handwork and time. ) The final result achieved was a set of methodologies and tools used to process a free text report, generating a XML document tagged with codes extracted from a medical terminology system. Considering all process steps, it was achieved a precision of at least 70%, in each step, a good score, if we consider that all the algorithms are rule based. In addiction to the NLP tools results, there are results concerning to medical ontologies evaluation for a pre-defined medical area, the organization need to make the ontologies usable by the NLP tools, the creation of a x-ray Corpus of reports in Portuguese and an information model used to document the reports. The Corpus could be used on the evaluation and test of NLP tools.

Os sistemas de informação hospitalares geram diariamente uma quantidade significativa de dados em formato de texto livre, principalmente através de laudos médicos. Os laudos geralmente são recuperados do sistema através de informações associadas, como identificação do paciente, por datas ou profissional responsável. A recuperação da informação a partir do conteúdo descritivo é uma tarefa não trivial, pois os sistemas hospitalares em geral não são capazes de verificar o conteúdo de um texto livre em uma busca. Não havendo uma estrutura básica de organização, categorização ou indexação do texto livre armazenado nas bases hospitalares, uma grande quantidade de informação deixa de estar disponível para profissionais que necessitam delas, pois não sabem como recuperá-las. A capacidade de recuperação do conhecimento armazenado nestas bases de dados seria de grande valia para pesquisadores, estudantes ou mesmo para o estudo de casos clínicos. Segundo o contexto descrito, este trabalho propõe a criação de uma ferramenta de documentação automática que tem por objetivo gerar uma formatação associada ao texto livre de laudos em radiologia através da adição de informações obtidas a partir de sistemas de terminologias médicos padronizados. Com este procedimento, pretende-se facilitar a pesquisa pelo conhecimento armazenado em uma base de dados médicos através da informação adicional gerada. Para tanto o trabalho envolve pesquisas nas áreas de Ontologias e Extração deInformação, uma subárea do Processamento de linguagem Natural. As ontologias são importantes neste trabalho por tratarem o problema da padronização das terminologias usadas na escrita dos laudos, bem como para fornecer a organização e formatação necessária para que os laudos passem a ser partes de uma base de conhecimento. ) A Extração de Informação fornece os algoritmos e técnicas necessárias para que os laudos sejam documentados de forma automática, minimizando a necessidade de intervenção humana, normalmente muito custosa em termos de trabalho manual e tempo. Como resultado final obteve-se um conjunto de metodologias e ferramentas capazes de receber um laudo em texto livre e gerar um documento XML rotulado com códigos de conceitos definidos em um sistema de terminologias médico, como o UMLS ou o Radlex. Em todas as fases de processamento, até a obtenção do arquivo XML de saída, obteve-se valores de precisão superiores a 70%, um resultado bastante satisfatório se considerado que os algoritmos de PLN utilizados são todos baseados em regras. Em adição às ferramentas de PLN desenvolvidas, cita-se como resultados, os trabalhos desenvolvidos para avaliação de ontologias médicas segundo uma área médica prédefinido, a organização das ontologias em um formato útil para a utilização por algoritmos de PLN, a criação de um Corpus de laudos de Raio-X de Tórax em português para treinamento e testes de aplicações de PLN e um modelo de informação para documentação dos laudos. / Hospital Information Systems generate each day a significant amount of data in free text format, mainly as medical reports. Normally the reports are recovered from the system through associated information like patient identification, dates or responsible identification, for example. To recover a report by its content is not a trivial task since hospital systems are not capable of searching the free text content. Without a basic organizational structure, some categorization and indexing the free text stored on the hospital database is not accessible, since it cannot be recovered in the right context when it is needed. The ability of recovering the knowledge stored on these databases would be valuable for researchers, students or for the study of clinical cases. According to the described context, this work considers the creation of a tool for automatic documentation of medical reports written in free text. The main objective is to format radiological reports to achieve a more efficient way of recovering the knowledge stored in medical report\'s databases. To achieve this goal, information from medical terminology systems is added to the original report automatically. Such task requires some research in the field of Ontologies and Information Extraction, a sub field of Natural Language Processing. Ontologies are important in this work because they provide the standardization needed for the terminologies used in the written reports. It is important too forsupplying the organization necessary to format the reports in an adequate way to be stored on the knowledge base. Information Extraction supplies the algorithms and the necessary techniques to register in an automatic way the radiological reports, minimizing the human intervention, normally with a high cost in terms of handwork and time. ) The final result achieved was a set of methodologies and tools used to process a free text report, generating a XML document tagged with codes extracted from a medical terminology system. Considering all process steps, it was achieved a precision of at least 70%, in each step, a good score, if we consider that all the algorithms are rule based. In addiction to the NLP tools results, there are results concerning to medical ontologies evaluation for a pre-defined medical area, the organization need to make the ontologies usable by the NLP tools, the creation of a x-ray Corpus of reports in Portuguese and an information model used to document the reports. The Corpus could be used on the evaluation and test of NLP tools.

This thesis establishes a connection between GOMMA and STROMA – both are tools of ontology processing. Consequently, a new workflow of denoting a set of correspondences with five semantic relation types has been implemented. Such a rich denotation is scarcely discussed within the literature. The evaluation of the denotation shows that trivial correspondences are easy to recognize (tF > 90). The challenge is the denotation of non-trivial types ( 30 < ntF < 70). A prerequisite of the implemented workflow is the extraction of semantic relations between concepts. These relations represent additional background knowledge for the enrichment tool STROMA and are integrated to the repository SemRep which is accessed by this tool. Thus, STROMA is able to calculate a semantic type more precisely. UMLS was chosen as a biomedical knowledge source because it subsumes many different ontologies of this domain and thus, it represents a rich resource. Nevertheless, only a small set of relations met the requirements which are imposed to SemRep relations. Further studies may analyze whether there is an appropriate way to integrate the missing relations as well. The connection of GOMMA with STROMA allows the semantic enrichment of a biomedical mapping. As a consequence, this thesis enlightens two subjects of research. First, STROMA had been tested with general ontologies, which models common sense knowledge. Within this thesis, STROMA was applied to domain ontologies. Studies have shown that overall, STROMA was able to treat such ontologies as well. However, some strategies for the enrichment process are based on assumption which are misleading in the biomedical domain. Consequently, further strategies are suggested in this thesis which might improve the type denotation. These strategies may lead to an optimization of STROMA for biomedical data sets. A more thorough analysis will review their scope, also beyond the biomedical domain. Second, the established connection may lead to deeper investigations about advantages of semantic enrichment in the biomedical domain as an enriched mapping is returned. Despite heterogeneity of source and target ontology, such a mapping results in an improved interoperability at a finer level of granularity. The utilization of semantically rich correspondences in the biomedical domain is a worthwhile focus for future research.

There is almost a universal agreement among scholars in information retrieval (IR) research that knowledge representation needs improvement. As core component of an IR system, improvement of the knowledge representation system has so far involved manipulation of this component based on principles such as vector space, probabilistic approach, inference network, and language modeling, yet the required improvement is still far from fruition. One promising approach that is highly touted to offer a potential solution exists in the cognitive paradigm, where knowledge representation practice should involve, or start from, modeling the human conceptual system. This study based on two related cognitive theories: the theory-based approach to concept representation and the psychological theory of semantic relations, ventured to explore the connection between the human conceptual model and the knowledge representation model (represented by samples of concepts and relations from the unified medical language system, UMLS). Guided by these cognitive theories and based on related and appropriate data-analytic tools, such as nonmetric multidimensional scaling, hierarchical clustering, and content analysis, this study aimed to conduct an exploratory investigation to answer four related questions. Divided into two groups, a total of 89 research participants took part in two sets of cognitive tasks. The first group (49 participants) sorted 60 food names into categories followed by simultaneous description of the derived categories to explain the rationale for category judgment. The second group (40 participants) performed sorting 47 semantic relations (the nonhierarchical associative types) into 5 categories known a priori. Three datasets resulted as a result of the cognitive tasks: food-sorting data, relation-sorting data, and free and unstructured text of category descriptions. Using the data analytic tools mentioned, data analysis was carried out and important results and findings were obtained that offer plausible explanations to the 4 research questions. Major results include the following: (a) through discriminant analysis category members were predicted consistently in 70% of the time; (b) the categorization bases are largely simplified rules, naïve explanations, and feature-based; (c) individuals theoretical explanation remains valid and stays stable across category members; (d) the human conceptual model can be fairly reconstructed in a low-dimensional space where 93% of the variance in the dimensional space is accounted for by the subjects performance; (e) participants consistently classify 29 of the 47 semantic relations; and, (f) individuals perform better in the functional and spatial dimensions of the semantic relations classification task and perform poorly in the conceptual dimension.