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Haute école de gestion de Genève

Practical implementation of a bridge between legacy EHR system and a clinical research environment

Vishnyakova, Dina ; Bottone, Sylviane ; Pasche, Emilie ; Lovis, Christian

In: Studies in Health Technology and Informatics, 2014, vol. 197, p. 29-33

Employing the bridge between Clinical Information System (CIS) and Clinical Research Environment (CRE) can provide functionality, which is not easily, implemented by traditional legacy EHR system. In this paper, the experience of such implementation at the University Hospitals of Geneva is described. General overview of the mapping of extracted from CIS data to the i2b2 Clinical Data Warehouse is...

Haute école de gestion de Genève

Development and tuning of an original search engine for patent libraries in medicinal chemistry

Pasche, Emilie ; Gobeill, Julien ; Kreim, Olivier ; Oezdemir-Zaech, Fatma ; Vachon, Thérèse ; Lovis, Christian ; Ruch, Patrick

In: BMC Bioinformatics, 2014, vol. 15, no. Suppl. 1, p. 1-9

Background. The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which intensively uses patent libraries for competitive intelligence and drug...

Haute école de gestion de Genève

Assisted knowledge discovery for the maintenance of clinical guidelines

Pasche, Emilie ; Ruch, Patrick ; Teodoro, Douglas ; Huttner, Angela ; Harbarth, Stephan ; Gobeill, Julien ; Wipfli, Rolf ; Lovis, Christian

In: PLoS One, 2013, vol. 8, no. 4, p. 1-11

Background: Improving antibiotic prescribing practices is an important public-health priority given the widespread antimicrobial resistance. Establishing clinical practice guidelines is crucial to this effort, but their development is a complex task and their quality is directly related to the methodology and source of knowledge used. Objective: We present the design and the evaluation of a tool...

Haute école de gestion de Genève

Use of controlled vocabularies to improve biomedical information retrieval tasks

Pasche, Emilie ; Gobeill, Julien ; Vishnyakova, Dina ; Ruch, Patrick ; Lovis, Christian

In: Studies in Health Technology and Informatics, 2013, vol. 192, p. 1068

The high heterogeneity of biomedical vocabulary is a major obstacle for information retrieval in large biomedical collections. Therefore, using biomedical controlled vocabularies is crucial for managing these contents. We investigate the impact of query expansion based on controlled vocabularies to improve the effectiveness of two search engines. Our strategy relies on the enrichment of users'...

Haute école de gestion de Genève

Utilization of ontology look-up services in information retrieval for biomedical literature

Vishnyakova, Dina ; Pasche, Emilie ; Lovis, Christian ; Ruch, Patrick

In: Studies in health technology and informatics, 2013, vol. 186, p. 155-159

With the vast amount of biomedical data we face the necessity to improve information retrieval processes in biomedical domain. The use of biomedical ontologies facilitated the combination of various data sources (e.g. scientific literature, clinical data repository) by increasing the quality of information retrieval and reducing the maintenance efforts. In this context, we developed Ontology...

Haute école de gestion de Genève

Interoperability driven integration of biomedical data sources

Teodoro, Douglas ; Choquet, Rémy ; Schober, Daniel ; Mels, Giovanni ; Pasche, Emilie ; Ruch, Patrick ; Lovis, Christian

In: Studies in health technology and informatics, 2011, vol. 169, p. 185-189

In this paper, we introduce a data integration methodology that promotes technical, syntactic and semantic interoperability for operational healthcare data sources. ETL processes provide access to different operational databases at the technical level. Furthermore, data instances have they syntax aligned according to biomedical terminologies using natural language processing. Finally, semantic...

Haute école de gestion de Genève

Building a transnational biosurveillance network using semantic web technologies : requirements, design, and preliminary evaluation

Teodoro, Douglas ; Pasche, Emilie ; Gobeill, Julien ; Emonet, Stéphane ; Ruch, Patrick ; Lovis, Christian

In: Journal of medical internet research, 2012, vol. 14, no. 3, p. 1-17

Background: Antimicrobial resistance has reached globally alarming levels and is becoming a major public health threat. Lack of efficacious antimicrobial resistance surveillance systems was identified as one of the causes of increasing resistance, due to the lag time between new resistances and alerts to care providers. Several initiatives to track drug resistance evolution have been developed....

Haute école de gestion de Genève

Using multimodal mining to drive clinical guidelines development

Pasche, Emilie ; Gobeill, Julien ; Teodoro, Douglas ; Vishnyakova, Dina ; Gaudinat, Arnaud ; Ruch, Patrick ; Lovis, Christian

In: Studies in health technology and informatics, 2011, vol. 169, p. 477-481

We present exploratory investigations of multimodal mining to help designing clinical guidelines for antibiotherapy. Our approach is based on the assumption that combining various sources of data, such as the literature, a clinical datawarehouse, as well as information regarding costs will result in better recommendations. Compared to our baseline recommendation system based on a...