Integration of biomedical literature and databases

Integration of biomedical literature and databases

Lars Juhl JensenEMBL Heidelberg

why integration?

why biomedicine?

why literature?

why databases?

open access databases

a lot of them

Duncan Hull, nodalpoint.org

PubChem

19.2 million compounds

GenBank

85 million sequences

89 billion nucleotides

UniProt

5.6 million sequences

PDB

50000 protein structures

BINDBiomolecular Interaction Network Database

DIPDatabase of Interacting Proteins

MINTMolecular Interactions Database

IntAct

BioGRID

204000 interactions

too many

incomplete

literature mining

MEDLINE

17.9 million citations

too much to read

information retrieval

finding the papers

user-specified query

“yeast AND cell cycle”

stemming

yeast / yeasts

dynamic query expansion

yeast / S. cerevisiae

ranking

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

no tool will find it

entity recognition

identifying the substance(s)

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

Cdc28 yeast

Cdc28 cell cycle

synonyms list

orthographic variation

CDC28

Cdc28p

disambiguation

Cdc2

SDS

still too much to read

information extraction

formalizing the facts

co-mentioning

statistical methods

NLPNatural Language Processing

Gene and protein names

Cue words for entity recognition

Verbs for relation extraction

[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

yet another database

integration

augmented browsing

semantic tagging

association networks

curated knowledge

genomic context

phylogenetic profiles

gene neighborhood

experimental data

physical interactions

genetic interactions

literature mining

restricted access

Bayesian framework

summary

literature mining is good

data integration is better

open access

Acknowledgments

STRING & STITCH– Christian von Mering

– Michael Kuhn

– Manuel Stark

– Samuel Chaffron

– Philippe Julien

– Tobias Doerks

– Jan Korbel

– Berend Snel

– Martijn Huynen

– Peer Bork

Reflect– Evangelos Pafilis

– Michael Kuhn

– Sean O’Donoghue

– Reinhardt Schneider

Natural Language Processing– Jasmin Saric

– Rossitza Ouzounova

– Isabel Rojas

– Peer Bork