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BiTEM
Home
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 * Home
 * Projects
 * Resources
 * News
 * People
 * Jobs

BiTEM
 * Home Home
   Table of contents
    * Who we are...
    * Research areas

 * Projects
   Projects
    * Archive
      Archive
       * 2021
       * 2020
       * 2019
       * 2015
       * 2014
       * 2013
       * 2011
       * 2010
       * 2009
       * 2008
       * 2006
       * 2004
   
    * Categories
      Categories
       * CTI
       * European
       * HES/HEG
       * HORIZON Europe
       * ICT
       * Join Project
       * RCSO/ISNET
       * SNF

 * Resources
   Resources
    * Archive
      Archive
       * 2023
       * 2022
       * 2021
       * 2018
       * 2015

 * News
   News
    * Archive
      Archive
       * 2023

 * People
   People
    * Patrick Ruch
    * Alexandre Flament
    * Anaïs Mottaz
    * Déborah Caucheteur
    * Emilie Pasche
    * Jeevanthi Lyiana Pathirana
    * Julien Gobeill
    * Julien Knafou
    * Luc Mottin
    * Marie Kolsch
    * Paul van Rijen
    * Pierre André Michel
    * Former members
      Former members
       * Arnaud Gaudinat
       * David Issom
       * Dina Vishnyakova
       * Douglas Teodoro
       * Fabio Ricci
       * Frédéric Erhler
       * Gabriele Musillo
       * Hind Laghzali
       * Igor Milhit
       * Jia Li
       * Kamel Nebhi
       * Mathilde Panès
       * Nona Naderi

 * Jobs
   Jobs
    * Archive
      Archive
       * 2023
       * 2018

Last Changes
 * Professor position in information sciences at HES-SO / HEG Geneva22 Dec 2023
 * Main achievements of the group in 202322 Dec 2023
 * SIBiLS - Swiss Institute of Bioinformatics Literature Services01 Oct 2023
 * BiotXplorer - searching biotic interactions in the literature01 Oct 2023
 * BMJ and Findzebra use cases in a computable format31 Jan 2022
 * DisprotGUI31 Jan 2022
 * Variomes - A High Recall Search Engine to Support the Curation of Genomic
   Variants31 Jan 2022
 * AIRating - Artificial Intelligence to support the evidence-based rating of
   information01 Oct 2021
 * e-BioDiv - Open Biodiversity FAIR-ification Services for Biospecimens stored
   in Swiss Natural History Museums01 Sep 2021
 * eBioDiv - Literature services for BioDiversity01 Sep 2021
 * BICIKL - Biodiversity Community Integrated Knowledge Library01 Jun 2021
 * CHEM::AI - Predicting and Exploring Novel Chemical Spaces Using Artificial
   Intelligence01 Oct 2020
 * Swiss Personalized Oncology01 Apr 2019
 * CINECA - Common Infrastructure for National Cohorts in Europe, Canada, and
   Africa01 Jan 2019
 * Three research associate positions at SIB Text Mining / HES-SO, Geneva
   Switzerland23 Jul 2018
 * neXtA5 - Accelerating Annotation of Articles via Automated Approaches in
   neXtProt13 Jun 2018
 * UPCLASS - UniProt Classifier13 Jun 2018
 * EXPAND Comparator12 Nov 2015
 * WeIRD - Web Intelligence for Rare Disease15 Jun 2015
 * EXPAND14 Sep 2014


BITEM GROUP


WHO WE ARE...

The BiTeM Group, headed by Patrick Ruch, is part of the Information Science
Department of the HES-SO/HEG Geneva. It gathers a network of researchers
(computer scientists, biologists, bioinformaticians, MDs...) affiliated to
various research institutions in Geneva. More information about BiTeM can be
found on the SIB Text Mining web pages. The Text Mining group of the SIB Swiss
Institute of Bioinformatics, gathers BiTeM's infrastructure services for
biologists and biocurators.


RESEARCH AREAS

The BiTeM group is involved in several research projects, with a strong focus on
clinical and biological data. The main research areas developed are:

 1. Text Mining: sometimes alternately referred to as text data mining, roughly
    equivalent to text analytics, TM aims at deriving high-quality information
    out of textual contents. High-quality information is typically achieved
    through the dividing of patterns and trends via association or pattern
    learning. Knowledge intensive resources such as dictionaries, terminologies,
    ontologies and manually crafted rules play an important role in the domain.
    Text mining usually involves the process of structuring the unstructured or
    semi-structured input text to generate a more structured (or enriched)
    database. A typical text mining task includes (e.g. question-answering):
    information retrieval, named-entity recognition and information extraction.
    Quality in text mining usually refers to some combination of relevance,
    novelty, and interestingness. Other common tasks include text categorization
    (filtering, descriptor assignment...), sentiment analysis, document
    summarization, and entity relation modeling (i.e., extraction of
    protein-protein interactions). Today many of these tasks are based on
    pre-trained language models, although data-poor approaches (e.g. information
    retrieval, rule-based methods, Support Vector Machines, ...) remain highly
    effective when data are sparse, as often in real case scenarii.

 2. Bibliomics: Bibliomics is the bioinformatics study of the bibliome. The
    bibliome is the totality of biological text corpus. It emphasizes the
    importance of biological text contents for biomedical sciences. In practice,
    bibliomics is often regarded as the application of textual data mining to
    literature in molecular biology and to MEDLINE in particular. However, the
    notion tends to expand beyond literature to various other contents, such as
    the web, patent documents or clinical reports. Thus, from the bibliome,
    biologists and computer scientists datamine to discover new gene targets and
    drugs, or explore biotic interactions. Under the umbrella of the SIB Swiss
    Institute of Bioinformatics and tanks to the Elixir Data Platform, the group
    maintains several literature services to support curators. In particular we
    develop triage instruments to help biologists and clinicians to efficiently
    access MEDLINE, PubMedCentral or the ClinicalTrials.gov.


GROUP MEMBERS


PATRICK RUCH

Professor at HEG / HESSO Geneva and Group Leader at SIB (Text Mining group)
Email


ALEXANDRE FLAMENT

 
Email


ANAÏS MOTTAZ

 
Email


DÉBORAH CAUCHETEUR

Scientific collaborator
Email


EMILIE PASCHE

 
Email


JEEVANTHI LYIANA PATHIRANA

 
Email


JULIEN GOBEILL

 
Email


JULIEN KNAFOU

 
Email


LUC MOTTIN

 
Email


MARIE KOLSCH

 
Email


PAUL VAN RIJEN

 
Email


PIERRE ANDRÉ MICHEL

 
Email


FORMER MEMBERS

 * Arnaud Gaudinat

 * David Issom

 * Dina Vishnyakova

 * Douglas Teodoro

 * Fabio Ricci

 * Frédéric Erhler

 * Gabriele Musillo

 * Hind Laghzali

 * Igor Milhit

 * Jia Li

 * Kamel Nebhi

 * Mathilde Panès

 * Nona Naderi

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