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Integration of biomedical literature and databases

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Lars Juhl Jensen
Lars Juhl Jensen

Nordic Conference for Scolarly Communication 2008, Scandic Star Hotel, Lund, Sweden, April 21-23, 2008

TecnologiaSaúde e medicina
1 de 106
Integration of biomedical literature and databases Lars Juhl Jensen EMBL 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
BIND Biomolecular Interaction Network Database
DIP Database of Interacting Proteins
MINT Molecular Interactions Database
IntAct
BioGRID
 
204000 interactions
too many
incomplete
literature mining
M EDLINE
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
NLP Natural Language Processing
[object Object],[object Object],[object Object],[object Object]
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 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 

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