Biomedical Informatics


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The Biomedical informatics research line gained a progressively larger role within XLDB and became a key topic, both within LaSIGE as well as externally, where the results achieved in ontology matching, semantic similarity, semantic web or machine learning methods for inference from molecular data have been published in the top journals in the area.

Key members of XLDB were in the organization committee of the FCT Funded PhD program BioSYS, and in the coordination of the Master in Bioinformatics and Computational Biology

Research spanned a wide range of topics, including but not limited to: semantic similarity, enrichment analysis, translational medicine, biomedical ontology engineering, genomic and proteomic data mining, natural language processing of biomedical literature and machine learning tools for structural pharmacology.

LASIGE was a General Member of the Virtual Physiological Human Network of Excelence.

Faculty: Francisco Couto (head), André Falcão, Dulce Domingos, Cátia Pesquita, Emanuel Santos,

Post-doctoral Researchers: Daniel Faria

Current Projects and Activities

  • SOMER : Semantic Ontology Matching using External Resources
  • SmartData : Turning Big Data into Smart Data (FLAD/NSF)
  • SPNET : In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
  • BiobankCloud : methodology to enable functional annotation of the sequences being stored in biobanks using cloud computing (as consultant)

Past Projects and Activities

  • AEB : Automated Extension of BioOntologies
  • ARN : Algorithms for the identification of genetic Regulatory Networks
  • ASSUME : Data mining methods for ASessing Similarity of molecular structUres in MEtric spaces
  • BOA : Biomedical Ontologies Applications
  • CoherenZy : Methods for Carbohydrate Enzyme Family Coherency Assessment
  • EPIWork : Developing the framework for an epidemic forecast infrastructure
  • FiBRE : Filtering Bioentity Recognition Errors
  • HCM : Integration and exploration of clinical and biological data concerning the disease hypertrophic cardiomyopathy (HCM)
  • ISPD : Information Systems for Pulmonary Diseases
  • Peptides : Peptidic programs for protein classification
  • ReBIL : Correlating enzyme sequences with their activity based on biological literature.
  • SABO : Semantic similarity across biomedical ontologies (VPH-NoE)
  • SOMER : Semantic Ontology Matching using External Resources
  • ThermInfo : Collecting, Retrieving, and Estimating Reliable Thermochemical Data
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