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Network integration of data and text
1.
Network integration of
data and text Lars Juhl Jensen
2.
Part 1 text
mining
3.
>10 km
4.
exponential growth
5.
6.
7.
law of diminishing
returns
8.
some things are
constant
9.
10.
~45 seconds per
paper
11.
computer
12.
as smart as
a dog
13.
teach it specific
tricks
14.
15.
16.
named entity recognition
17.
Reflect
18.
augmented browsing
19.
browser add-on
20.
Pafilis, O’Donoghue, Jensen
et al., Nature Biotechnology , 2009
21.
collaborations
22.
23.
web services
24.
25.
Utopia Documents
26.
information extraction
27.
co-mentioning
28.
29.
<10 hours
30.
no access
31.
Part 2 protein
networks
32.
STRING
33.
Szklarczyk, Franceschini et
al., Nucleic Acids Research , 2011
34.
630 genomes
35.
many databases
36.
genomic context
37.
gene fusion
38.
Korbel et al.,
Nature Biotechnology , 2004
39.
conserved neighborhood
40.
operons
41.
Korbel et al.,
Nature Biotechnology , 2004
42.
bidirectional promoters
43.
Korbel et al.,
Nature Biotechnology , 2004
44.
phylogenetic profiles
45.
Korbel et al.,
Nature Biotechnology , 2004
46.
experimental data
47.
physical interactions
48.
Jensen & Bork,
Science , 2008
49.
gene coexpression
50.
51.
curated knowledge
52.
pathways
53.
Letunic & Bork,
Trends in Biochemical Sciences , 2008
54.
text mining
55.
56.
many data types
57.
many databases
58.
different formats
59.
different identifiers
60.
variable quality
61.
quality scores
62.
calibrate vs. gold
standard
63.
von Mering et
al., Nucleic Acids Research , 2005
64.
orthology transfer
65.
Frishman et al.,
Modern Genome Annotation , 2009
66.
Part 3 small
molecule networks
67.
STITCH
68.
Kuhn et al.,
Nucleic Acids Research , 2010
69.
in vitro
binding assays
70.
text mining
71.
chemical similarity
72.
Campillos & Kuhn
et al., Science , 2008
73.
similar drugs share
targets
74.
Campillos & Kuhn
et al., Science , 2008
75.
only trivial predictions
76.
phenotypic similarity
77.
chemical perturbations
78.
phenotypic readouts
79.
drug treatment
80.
side effects
81.
no database
82.
package inserts
83.
Campillos & Kuhn
et al., Science , 2008
84.
text mining
85.
manual validation
86.
side-effect correlations
87.
Campillos & Kuhn
et al., Science , 2008
88.
side-effect frequencies
89.
Campillos & Kuhn
et al., Science , 2008
90.
raw similarity score
91.
Campillos & Kuhn
et al., Science , 2008
92.
p-values
93.
Campillos & Kuhn
et al., Science , 2008
94.
side-effect similarity
95.
chemical similarity
96.
Campillos & Kuhn
et al., Science , 2008
97.
drug–drug network
98.
Campillos & Kuhn
et al., Science , 2008
99.
categorization
100.
Campillos & Kuhn
et al., Science , 2008
101.
20 drug–drug pairs
102.
in vitro
binding assays
103.
K i <10
µM for 11 of 20
104.
cell assays
105.
9 of 9
showed activity
106.
107.
larsjuhljensen
108.
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