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Haute école de gestion de Genève

Using a question-answering approach in machine reading task of biomedical texts about the Alzheimer disease

Vishnyakova, Dina ; Gobeill, Julien ; Ruch, Patrick

In: Working Notes for CLEF 2013 Conference, Valencia, Spain, September 23-26, 2013., 2013, vol. 1179, p. 1-6

For the machine-reading task of biomedical texts about the Alz-heimer disease we have used a Question-Answering approach by adapting func-tionalities of Question-Answering (Q-A) engine EAGLi. We didn’t involve any other Natural Language Processing method. As a knowledge store we used the biggest resource of biomedical literature - MEDLINE. Our final results showed that the best run was without...

Haute école de gestion de Genève

Instance-based learning for tweet categorization in CLEF REPLAB 2014

Gobeill, Julien ; Gaudinat, Arnaud ; Ruch, Patrick

In: Proceedings of Conference and Labs of the Evaluation Forum (CLEF), 2014, p. 1491-1499

BiTeM/SIBtex is a university research group with a strong background in Text Mining and Bibliomics, and a long tradition of participating in large evaluation campaigns. The CLEF RepLab 2014 Track was the occasion to integrate several local tools into a complete system for tweet monitoring and categorization based on instance-based learning. The algorithm we implemented was a k Nearest Neighbors....

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

Electronic processing of informed consents in a global pharmaceutical company environment

Gobeill, Julien ; Ruch, Patrick ; et al.

In: Studies in health technology and informatics, 2013, vol. 205, p. 995-999

We present an electronic capture tool to process informed consents, which are mandatory recorded when running a clinical trial. This tool aims at the extraction of information expressing the duration of the consent given by the patient to authorize the exploitation of biomarker-related information collected during clinical trials. The system integrates a language detection module (LDM) to route a...

Haute école de gestion de Genève

Overview of the gene ontology task at BioCreative IV

Gobeill, Julien ; Ruch, Patrick ; et al.

In: Database : the journal of biogical database and curation, 2014, p. 14

Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly...

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

Improving data and knowledge management to better integrate health care and research

Cases, Montserrat ; Furlong, Laura I. ; Albanell, Joan ; Altman, Russ B. ; Bellazzi, Riccardo ; Boyer, Scott ; Brand, Angela ; Brookes, Anthony J. ; Brunak, Soren ; Clark, Timothy W. ; Gea, Joaquim ; Ghazal, Peter ; Graf, Norbert ; Guigo, Roderic ; Klein, Teri E. ; Lopez-Bigas, Nuria ; Maojo, Victor ; Mons, Barend ; Musen, Mark ; Oliveira, José L. ; Rowe, Anthony ; Ruch, Patrick ; Shabo, Amnon ; Shortliffe, Edward H. ; Valencia, Alfonso ; van der Lei, Johan ; Mayer, Miguel A. ; Sanz, Ferran

In: Journal of internal medicine, 2013, vol. 274, no. 4, p. 321-328

Medicine is an increasingly data intensive discipline, with a growing need to link individual patient health records to rapidly changing research knowledge for better differential diagnosis, prognosis, and prediction of treatment response. Equally, biomedical research will gain massively from the integrative analysis of clinical and multi-omics information. Capitalizing on these opportunities...

Haute école de gestion de Genève

Application of text-mining for updating protein post-translational modification annotation in UniProtKB

Veuthey, Anne-Lise ; Bridge, Alan ; Gobeill, Julien ; Ruch, Patrick ; McEntyre, Johanna R. ; Bougueleret, Lydie ; Xenarios, Ioannis

In: BMC Bioinformatics, 2013, vol. 14, p. 104-113

Background: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature...

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...