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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

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

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

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

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...

Haute école de gestion de Genève

Bitem group report for TREC chemical IR track 2011

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

In: TREC 2011, 2011, p. s.p.

For the third year, the BiTeM group participated in the TREC Chemical IR Track. For this campaign, we applied strategies that already showed their effectiveness, as the Citations Feedback, which takes benefit from the citations of the retrieved documents in order to re-arrange the ranking. But we also investigated a new inter-lingua model built with chemical annotations with concepts that we...

Haute école de gestion de Genève

The gene normalization task in BioCreative III

Lu, Zhiyong ; Kao, Hung-Yu ; Wei, Chih-Hsuan ; Huang, Minlie ; Liu, Jingchen ; Kuo, Cheng-Ju ; Hsu, Chun-Nan ; Tzong-Han Tsai, Richard ; Dai, Hong-Jie ; Okazaki, Naoaki ; Cho, Han-Cheol ; Gerner, Martin ; Solt, Illes ; Agarwal, Shashank ; Liu, Feifan ; Vishnyakova, Dina ; Ruch, Patrick ; Romacker, Martin ; Rinaldi, Fabio ; Bhattacharya, Sanmitra ; Srinivasan, Padmini ; Liu,Hongfang ; Torii, Manabu ; Matos, Sergio ; Campos, David ; Verspoor, Karin ; M Livingston, Kevin ; Wilbur, W John

In: BMC Bioinformatics, 2011, vol. 12, p. 1-19

Background: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain...