Skip to content

Commit 82d7160

Browse files
NiMaZiNiMaZi
committed
with data sample
1 parent 887c0bb commit 82d7160

File tree

6 files changed

+3087
-10
lines changed

6 files changed

+3087
-10
lines changed

‎.gitignore

-10
Original file line numberDiff line numberDiff line change
@@ -1,10 +0,0 @@
1-
2-
ontology_depth2word.pkl
3-
4-
*.pkl
5-
6-
*.pkl
7-
8-
*.csv
9-
10-
log.txt

‎data_sample/ConCode2Vid.json

+1
Large diffs are not rendered by default.

‎data_sample/sample/abs0.csv

+100
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,100 @@
1+
Mention,ConceptCode,ConceptName,SemanticType,Start
2+
Tumors,C98275,Tumor Mass,Finding,0
3+
exhibit,C96979,Exhibit,Intellectual Product,7
4+
heterogeneity,C28359,Heterogeneity,Qualitative Concept,23
5+
immunohistochemistry,C16722,Immunohistochemistry,Laboratory Procedure,55
6+
IHC,C23020,Immunohistochemistry Staining Method,Laboratory Procedure,77
7+
staining,C50753,Staining,Finding,82
8+
patterns,C25336,Pattern,Spatial Concept,91
9+
Current,C25471,Current,Temporal Concept,101
10+
IHC,C23020,Immunohistochemistry Staining Method,Laboratory Procedure,109
11+
quantification,C48937,Quantitation,Activity,113
12+
methods,C71460,Method,Conceptual Entity,128
13+
information,C48191,Information,Conceptual Entity,141
14+
heterogeneity,C28359,Heterogeneity,Qualitative Concept,170
15+
each,C64933,Each,Qualitative Concept,187
16+
whole,C25326,Whole,Qualitative Concept,192
17+
slide,C25325,Slide,Manufactured Object,198
18+
image,C48179,Image,Entity,204
19+
fields view,C74298,Field of View,Spatial Concept,232
20+
single,C48440,Single,Qualitative Concept,252
21+
staining,C50753,Staining,Finding,259
22+
index,C25390,Index,Intellectual Product,268
23+
aim,C60761,Aim,Conceptual Entity,279
24+
study,C63536,Study,Research Activity,291
25+
sensitivity,C25201,Sensitivity,Quantitative Concept,320
26+
IHC,C23020,Immunohistochemistry Staining Method,Laboratory Procedure,338
27+
quantification,C48937,Quantitation,Activity,342
28+
method,C71460,Method,Conceptual Entity,357
29+
uses,C107498,Useful,Qualitative Concept,369
30+
heterogeneity,C28359,Heterogeneity,Qualitative Concept,379
31+
compare,C49156,Comparison,Activity,405
32+
IHC,C23020,Immunohistochemistry Staining Method,Laboratory Procedure,413
33+
staining,C50753,Staining,Finding,417
34+
patterns,C25336,Pattern,Spatial Concept,426
35+
grid,C70846,Grid,Manufactured Object,471
36+
square,C48350,Square Shape,Qualitative Concept,479
37+
computed,C61298,Computation,Activity,497
38+
staining,C50753,Staining,Finding,510
39+
index,C25390,Index,Intellectual Product,519
40+
distributions,C45273,Distribution,Activity,525
41+
quantify,C48937,Quantitation,Activity,542
42+
heterogeneities,C28359,Heterogeneity,Qualitative Concept,551
43+
samples,C70699,Biospecimen,Body Substance,576
44+
distributions,C45273,Distribution,Activity,595
45+
inputs,C47905,Input,Conceptual Entity,612
46+
non,C25594,Negation,Functional Concept,622
47+
statistical,C17167,Statistics,Occupation or Discipline,637
48+
comparisons,C49156,Comparison,Activity,649
49+
applied,C113519,Apply,Activity,665
50+
grid,C70846,Grid,Manufactured Object,677
51+
method,C71460,Method,Conceptual Entity,682
52+
fixed,C84514,Fixed Specimen,Body Substance,692
53+
tumor samples,C18009,Tumor Tissue,Tissue,698
54+
26,C126886,Twenty Six,Quantitative Concept,717
55+
obtained,C52349,Obtain,Activity,727
56+
double blind study,C15228,Double Blind Study,Research Activity,743
57+
preclinical study,C48678,Nonclinical Study,Research Activity,756
58+
patient derived xenograft model,C122936,Patient Derived Xenograft,Experimental Model of Disease,779
59+
orthotopic,C94384,Orthotopic,Qualitative Concept,795
60+
pediatric,C14154,Pediatric,Temporal Concept,825
61+
neuroblastoma,C3270,Neuroblastoma,Neoplastic Process,835
62+
CD1,C114988,CD1 Glycoprotein,Classification,852
63+
nude,C14239,Nude Mouse,Mammal,856
64+
mice,C14238,Mouse,Mammal,861
65+
compared,C49156,Comparison,Activity,870
66+
results,C20200,Outcome,Finding,883
67+
grid,C70846,Grid,Manufactured Object,898
68+
method,C71460,Method,Conceptual Entity,903
69+
results,C20200,Outcome,Finding,917
70+
based,C48055,Base,Qualitative Concept,925
71+
whole,C25326,Whole,Qualitative Concept,934
72+
slide,C25325,Slide,Manufactured Object,940
73+
indices,C50001,Indicator Device Component,Manufactured Object,946
74+
current,C25471,Current,Temporal Concept,959
75+
grid,C70846,Grid,Manufactured Object,994
76+
method,C71460,Method,Conceptual Entity,999
77+
detects,C111567,Detectable,Clinical Attribute,1015
78+
alterations,C28344,Alteration,Conceptual Entity,1034
79+
other,C17649,Other,Qualitative Concept,1051
80+
tests,C47891,Test,Activity,1057
81+
based,C48055,Base,Qualitative Concept,1063
82+
whole,C25326,Whole,Qualitative Concept,1072
83+
slide,C25325,Slide,Manufactured Object,1078
84+
indices,C50001,Indicator Device Component,Manufactured Object,1084
85+
Based,C48055,Base,Qualitative Concept,1108
86+
robustness,C94972,Robust,Qualitative Concept,1117
87+
increased sensitivity,C63078,Increased Device Sensitivity,Event,1132
88+
increased sensitivity,C73503,Increased Sensitivity,Phenomenon or Process,1132
89+
statistical,C17167,Statistics,Occupation or Discipline,1157
90+
inference,C75591,Inference,Activity,1169
91+
method,C71460,Method,Conceptual Entity,1201
92+
whole,C25326,Whole,Qualitative Concept,1211
93+
slide,C25325,Slide,Manufactured Object,1217
94+
grid,C70846,Grid,Manufactured Object,1223
95+
quantification,C48937,Quantitation,Activity,1228
96+
superior,C25235,Superior,Spatial Concept,1246
97+
whole,C25326,Whole,Qualitative Concept,1267
98+
slide,C25325,Slide,Manufactured Object,1273
99+
quantification,C48937,Quantitation,Activity,1279
100+
techniques,C16847,Technique,Activity,1294

‎data_sample/sample/abs1.csv

+23
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,23 @@
1+
Mention,ConceptCode,ConceptName,SemanticType,Start
2+
Cardiopulmonary,C13362,Cardiopulmonary,"Body Part, Organ, or Organ Component",0
3+
interactions,C54708,Drug Interaction,Phenomenon or Process,16
4+
present,C25626,Present,Qualitative Concept,33
5+
humans,C14225,Human,Human,64
6+
normal,C14165,Normal,Conceptual Entity,76
7+
cardiac,C13306,Cardiac,Qualitative Concept,83
8+
respiratory,C25656,Respiratory,Body System,95
9+
function,C25518,Function,Conceptual Entity,107
10+
presence,C25626,Present,Qualitative Concept,133
11+
significant,C41130,Significant,Functional Concept,145
12+
impairment,C21055,Impairment,Idea or Concept,157
13+
system cardiovascular,C35552,Cardiovascular System Finding,Finding,178
14+
between,C94545,Between,Qualitative Concept,218
15+
pulmonary,C13304,Pulmonary,Qualitative Concept,245
16+
review,C42729,Review,Activity,290
17+
discuss,C71323,Discussion,Organism Function,302
18+
physiologic,C17650,Physiologic,Qualitative Concept,314
19+
consequences,C74555,Consequence,Phenomenon or Process,344
20+
interactions,C54708,Drug Interaction,Phenomenon or Process,366
21+
patients,C53691,Veterinary Patient,Organism,382
22+
heart failure,C50577,Heart Failure,Disease or Syndrome,396
23+
heart failure,C50577,Heart Failure,Disease or Syndrome,396

0 commit comments

Comments
 (0)