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

Kristina Hettne

Antoinne van Veldhoven

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

What do we do? – Ontology assembly

Entrez Gene Swiss-Prot HUGO

Combination

Add spelling variations

Remove highly ambiguous terms

What do we do? – Concept tagging

MEDLINE text Malaria fever is a disease.

Concept profile of text

C24530 1

C12634 0.5

Concept Weight

Identify concepts* Malaria fever is a disease.

C24530 C12634*homonym disambiguation!

What do we do? – Concept profile creation

TextTextText Concept

Concept profile of textConcept profile of textConcept profile of text Concept profile of concept

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

What do we do? – Comparing concept profiles

What do we do? – Analysis of comparison

Concept Name Weight RAB27B MYRIP MLPH RAB27A

RAB27A 52.17 0.61 0.74 0.73 1

MLPH 11.16 - 0.44 1 0.29

Myosin Type V 7.22 0.04 0.68 0.4 0.22

Melanosomes 6.7 0.12 0.3 0.47 0.27

RAB27B 4.06 1 0.14 - 0.11

MYRIP 2.98 0.07 1 0.09 0.06

Melanocytes 2.73 0.13 0.14 0.28 0.17

Myosins 2.33 0.04 0.38 0.22 0.12

Myosin Heavy Chains 1.72 - 0.46 0.18 0.09

GTP Phosphohydrolases 1.31 0.17 0.23 0.04 0.08

Actins 1.17 0.05 0.32 0.12 0.06

Exocytosis 0.87 0.08 0.12 0.08 0.12

Secretory Vesicles 0.68 0.07 0.16 0.06 0.09

Carrier Proteins 0.59 - 0.11 0.17 0.09

Organelles 0.54 0.11 - 0.12 0.09

rab GTP-Binding Proteins 0.52 0.16 - 0.04 0.12

What do we do? – Nucleolar proteome Function unknow nChaperonesChromatin structureFibrous proteinsmRNA metabolismOthersRibosomal proteinsRibosome biogenesisTranslation

SRP9PARN

40S ribosomal protein S27a

Exosome comp. 10

O43390P98179

Q8N220

Who are we working with?

Biologists

ErasmusMC (urology, hematology)

Leiden University Medical Center (human genetics)

Others

Knewco

Collexis

Our website

www.biosemantics.org