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Literature mining and large-scale data integration Lars Juhl Jensen EMBL Heidelberg
literature mining
why?
 
too much to read
information retrieval
finding the papers
ad hoc  retrieval
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
good synonyms list
manual curation
orthographic variation
CDC28
Cdc28p
disambiguation
hairy
SDS
APC
Cdc2
 
 
 
 
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
 
no new discoveries
text mining
undiscovered links
 
Raynaud’s syndrome
fish oil
 
temporal trends
 
buzzwords
 
data integration
association networks
 
information extraction
 
curated knowledge
 
protein interaction data
 
genetic interaction data
 
gene expression data
 
computational predictions
conserved neighborhood
 
gene fusion
 
phylogenetic profiles
 
variable reliability
raw quality scores
 
 
 
not comparable
benchmarking
calibrate vs. gold standard
 
probabilistic scores
spread over many species
373 genomes
 
transfer by orthology
 
combine all evidence
P = 1-(1-P 1 ) . (1-P 2 ) . (1-P 3 ) …
web resources
 
 
signaling networks
phosphoproteomics
 
in vivo  phosphosites
kinases are unknown
computational methods
 
overprediction
context
scaffolders
association networks
 
NetworKIN
 
benchmarking
 
2.5-fold better accuracy
web resources
 
 
summary
literature mining is good
data integration is better
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],[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]
http://larsjuhljensen.wordpress.com

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Literature mining and large-scale data integration