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Biosemantics group

Biosemantics group. Martijn Schuemie. Overview. Who are we? What do we do? Who are we working with?. Who are we?. ErasmusMC University Medical Center Rotterdam Department of Medical Informatics Biosemantics group Jan Kors Barend Mons Erik van Mulligen Martijn Schuemie Rob Jelier

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Biosemantics group

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  1. Biosemantics group Martijn Schuemie

  2. Overview • Who are we? • What do we do? • Who are we working with?

  3. Who are we? • ErasmusMC University Medical Center Rotterdam • Department of Medical Informatics • Biosemantics group • Jan Kors • Barend Mons • Erik van Mulligen • Martijn Schuemie • Rob Jelier • Kristina Hettne • Antoinne van Veldhoven

  4. What do we do? Biosemantics • Molecular Biology • High throughput experiment data (genomics and proteomics) • Gene and protein databases, MEDLINE, Gene Ontology Biosemantics • Concept-based text-mining • Interpretation of experiment data • Knowledge discovery

  5. Entrez Gene Swiss-Prot HUGO Combination What do we do? – Ontology assembly Add spelling variations Remove highly ambiguous terms

  6. Malaria fever is a disease. MEDLINE text Identify concepts* Malaria fever is a disease. *homonym disambiguation! C24530 C12634 Concept profile of text Concept Weight C24530 1 C12634 0.5 What do we do? – Concept tagging

  7. Text Text Text Concept Concept profile of text Concept profile of text Concept profile of text Concept profile of concept What do we do? – Concept profile creation

  8. What do we do? – Concept profiles of everything! Profile of gene ESR1: estrogen receptor 1 breast neoplasm 0.5 BRCA1 0.34 PGR 0.30 Estrogen 0.28 BRCA2 0.25 TP53 0.15 gene suppressor tumor 0.12 genetics polymorphism 0.12 genetic predisposition to disease 0.10 female 0.05

  9. What do we do? – Comparing concept profiles

  10. What do we do? – Analysis of comparison

  11. 40S ribosomal protein S27a Exosome comp. 10 P98179 O43390 SRP9 PARN Q8N220 What do we do? – Nucleolar proteome

  12. Who are we working with? Biologists • ErasmusMC (urology, hematology) • Leiden University Medical Center (human genetics) Others • Knewco • Collexis

  13. Our website www.biosemantics.org

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