This page contains supplementary information to accompany the paper:
Connecting the Dots between PubMed Abstracts
M. Shahriar
Hossain1, Joseph Gresock1, Yvette Edmonds2,
Richard Helm2, Malcolm Potts3, Naren
Ramakrishnan1
1Dept. of Computer Science,
Virginia Tech, Blacksburg, VA 24061, USA
2Dept. of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
3Dept. of Biological and Environmental Sciences, Qatar University,
Qatar
|
# of Stories |
Case Study 1 |
Case Study 2 |
Case Study 3 |
|
After A* search |
332,104 |
74,893 |
119,964 |
|
After
p and q-value filtering ( |
17,266 |
6,486 |
11,739 |
|
After context filtering |
611 |
424 |
202 |
|
After Sentence cohesion filtering |
159 |
135 |
48 |
The table above provides statistics
about the stories after each important stage of the storytelling pipeline. It
shows that initially we obtained 332,104 stories for case study 1, 74,893
stories for case study 2, and 119,964 stories for case study 3. We filter the
stories based on statistical significance (
, 
) and obtained 17266, 6486, and 11739 stories
respectively for case study 1, 2, and 3. For case study 1, we obtain 611
stories after the context overlap filtering and 159 final stories after
sentence cohesion filtering. For case study 2, we had 424 stories after
applying the context filter and 135 final stories after sentence cohesion
filtering. The number of stories after context filtration for case study 3 is 202,
while the final set contained 48 stories. The generated stories can be found in
the following three links:
Case
study 1 Case
study 2 Case
study 3
|
Case
study |
Molecule |
Query |
|
Case study
1 |
IL-1
alpha |
"IL-1+alpha+OR+IL-1alpha+OR+Interleukin-1+alpha+OR+Interleukin-1alpha" |
|
IL-1+beta |
"IL-1+beta+OR+IL-1beta+OR+Interleukin-1+beta+OR+Interleukin-1beta" | |
|
IL-6 |
"IL-6+OR+Interleukin-6" | |
|
IL-8 |
"IL-8+OR+Interleukin-8" | |
|
IL-13 |
"IL-13+OR+Interleukin-13" | |
|
IL-24 |
"IL-24+OR+Interleukin-24" | |
|
MMP |
"matrix+metalloproteinase" | |
|
CD38 |
"CD38" | |
|
MCP-2 |
"MCP-2+OR+chemokine+ccl8+OR+chemokine" | |
|
IFN-gamma |
"IFN-gamma+OR+interferon+gamma+OR+IFNG+OR+IFN-G" | |
|
Stanniocalcin |
"stanniocalcin+OR+teleocalcin" | |
|
serpinB2 |
"serpinB2+OR+plasminogen+activator+inhibitor-2+OR+PAI-2" | |
|
IGF-1 |
"IGF-1+OR+IGF1+OR+insulin-like+growth+factor+1" | |
|
MCP1 |
"MCP1+OR+MCP-1+OR+monocyte+chemotactic+protein+1" | |
|
Nicotinamide |
"nicotinamide+OR+niacinamide+OR+niacin" | |
|
MMP-3 |
"MMP-3+OR+MMP3+OR+matrix+metallopeptidase+3" | |
|
SFRP1 |
"SFRP1+OR+SFRP-1+OR+secreted+frizzled-related+protein+1" | |
|
MMP12 |
"MMP12+OR+MMP-12+OR+matrix+metallopeptidase+12" | |
|
CXCL1 |
"CXCL1+OR+CXCL-1", | |
|
Poly(ADP-ribose) |
"poly-ADP-ribose+OR+pADP+ribose+OR+poly+adenosine+diphosphate+ribose" | |
|
Case study
2 |
IL-1 |
"IL-1+beta+OR+IL-1beta+OR+Interleukin-1+beta+OR+Interleukin-1beta" |
|
IL-8 |
"IL-8+OR+Interleukin-8" | |
|
TNF-alpha |
"TNF-alpha+OR+tumour+necrosis+factor+alpha+OR+TNFalpha" | |
|
IFN-gamma |
"IFN-gamma+OR+interferon+gamma+OR+IFNG+OR+IFN-G" | |
|
NF-KB |
"NF-KB+OR+NF-kappa-B" | |
|
CREB |
"CREB+OR+Cyclic-AMP+response+element+binding+protein" | |
|
JunD |
"JunD+OR+jun+D+proto-oncogene" | |
|
ATF2 |
"ATF2+OR+activating+transcription+factor+2" | |
|
ATF3 |
"ATF3+OR+activating+transcription+factor+3" | |
|
STAT1 |
"STAT1+OR+signal+transducer+and+activator+of+transcription+1" | |
|
STAT2 |
"STAT2+OR+signal+transducer+and+activator+of+transcription+2+OR+stat2+transcription+factor" | |
|
c-jun |
"c-jun+OR+c-jun+transcription+factor+OR+jun+genes" | |
|
c-fos |
"c-fos+OR+proto-oncogene+proteins+c-fos+OR+fos+genes" | |
|
BRCA1 |
"BRCA1+OR+breast+cancer+1+OR+brca1+genes+OR+brca1+protein" | |
|
Case study
3 |
Glutamine |
"glutamine" |
|
PKM2 |
"PK-M2+OR+PKM2+OR+pyruvate+kinase+muscle+isozyme+
OR+PKM+OR+pyruvate+kinase+type+K" | |
|
OIP3 |
"OIP3" | |
|
CTHBP |
"cytosolic+thyroid+hormone-binding+protein+OR+CTHBP" | |
|
Pyruvate
kinase |
"pyruvate+kinase" |
