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BITEM Projects

GOAssay - Gene Ontology Annotation of PubChem Assays

A joint collaboration with the University of Indiana.

An experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model.

See 1

  1. Rajarshi Guha, Julien Gobeill, and Patrick Ruch. Goassay: from gene ontology to assays identifiers - towards automatic functional annotation of pubchem bioassays. Nature Precedings, Apr 2009. URL: https://doi.org/10.1038/npre.2009.3176.1, doi:10.1038/npre.2009.3176.1. ↩↩↩

epSOS - Smart Open Services for European Patients

epSOS – Smart Open Services for European Patients - is the main European electronic Health (eHealth) interoperability project co-funded by the European Commission and the partners. It focuses on improving medical treatment of citizens while abroad by providing health professionals with the necessary patient data.

BiND - Biomedical Novelty Detection

Background hypothesis. In existing search engines, including the most advanced question-answering architectures, such as EAGLi, answers or documents are provided to the user some relevance-driven ranking criteria. However, providing a ranked list of documents or answers is not sufficient regarding novelty detection; therefore being able to decide whether the retrieved answer is new would provide a major improvement, which could impact the intrinsic definition of relevance. Aims.

DebugIT

DebugIT

The DebugIT project is a large-scale integrating project funded within the 7th EU Framework Programme (FP7). The main objectives are to build IT tools that should have significant impacts for the monitoring and control of infectious diseases and antimicrobial resistances in Europe. This will be realized by building a technical and semantic infrastructure able to:

  • share heterogeneous clinical data sets from different hospitals in different countries, with different languages and legislations
  • analyze large amounts of this clinical data with advanced multimedia data mining
  • apply the obtained knowledge for clinical decisions and outcome monitoring.

UniMed - From UniProt to Medecine

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A joint project with the Swiss-Prot research group The Unimed project addresses the important problem of increasing interoperability between data resources from the medical informatics and the bioinformatics domains. We propose to link UniProtKB entries to the two most widely used disease terminologies:

  • ICD-10, which is the official disease classification provided by the WHO,
  • MeSH, which is the controlled vocabulary thesaurus used for biomedical and health-related document indexing.

12

  1. Anaïs Mottaz, Yum L Yip, Patrick Ruch, and Anne-Lise Veuthey. Mapping protein information to disease terminologies. Journal of Integrative Bioinformatics, 4(3):243–251, 2007. ↩↩

  2. Ruch Patrick, Mottaz Anaïs, Veuthey Anne-Lise, and others. Mapping proteins to disease terminologies: from uniprot to mesh. BMC Bioinformatics, 2008. ↩↩

  • in SNF

EAGL - Engine for question Answering in Genomic Literature

EAGL

The goal of this joint project between the Swiss-Prot group of the Swiss Institute of Bioinformatics and the Medical Informatics Service of the University Hospital of Geneva is to explore the development of question-answering systems in functionalgenomics.

SemanticMining

SemanticMining

The European Network of Excellence for Biomedical Data Mining and Semantic Interoperability aims at bridging gaps in European research infrastructure and facilitating cross-fertilisation between scientific disciplines such as computer science, system engineering and medical/clinical research. The long-term goal of the network is the development of generic methods and tools supporting critical tasks in medical and biomedical informatics, such as, data-mining, knowledge discovery, knowledge representation, abstraction and indexing of information, semantic-based information retrieval in a complex and high-dimensional information space, and knowledge based adaptive systems for provision of decision support for dissemination of evidence based medicine.