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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

Full-texts representations with medical subject headings, and co-citations network reranking strategies for TREC 2014 clinical decision support track

Gobeill, Julien ; Gaudinat, Arnaud ; Pasche, Emilie ; Ruch, Patrick

In TREC 2014 Clinical Decision Support Track, the task was to retrieve full-texts relevant for answering generic clinical questions about medical records. For this purpose, we investigated a large range of strategies in the five runs we official-ly submitted. Concerning Information Retrieval (IR), we tested two different indexing levels: documents or sections. Sec-tion indexing was clearly below...

Haute école de gestion de Genève

Closing the loop : from paper to protein annotation using supervised Gene Ontology classification

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

In: Database : the journal of biogical database and curation, 2014, p. 7

Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow of publications. In 2004, the first BioCreative challenge already designed a task of automatic GO concepts assignment from a full text. At this time, results were judged far from reaching the...

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

BiTeM/SIBtex group proceedings for BioCreative IV, Track 4 : Gene Ontology curation

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

In: Proceedings of the 4th BioCreative Challenge Evaluation Workshop, 2013, vol. 1, p. 108-113

For the BioCreative IV Track 4, we exploited the power of our machine learning Gene Ontology classifier, GOCat. GOCat computes similarities between an input text and already curated instances in order to infer GO terms. GO Annotations (GOA) and MEDLINE are used for populating the knowledge base (almost 100000 curated abstracts). For the subtask A, we designed a state-of-the-art statistical...

Haute école de gestion de Genève

Managing the data deluge : data-driven GO category assignment improves while complexity of functional annotation increases

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

In: Database (Oxford), 2013, p. 1-9

The available curated data lag behind current biological knowledge contained in the literature. Text mining can assist biologists and curators to locate and access this knowledge, for instance by characterizing the functional profile of publications. Gene Ontology (GO) category assignment in free text already supports various applications, such as powering ontology-based search engines, finding...

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

ToxiCat : hybrid named entity recognition services to support curation of the Comparative Toxicogenomic Database

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

In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, 2013, vol. 1, p. 108-113

We report on the original implementation of named entity recognition (NER) modules based on an automatic text categorization pipeline, so-called ToxiCat (Toxicogenomic Categorizer), developed to perform biomedical documents classification and prioritization for the previous Biocreative campaign in order to speed up the curation of the Comparative Toxicogenomics Database (CTD). ToxiCat NER modules...

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...