Back

Classifying Literature Extracted Events for Automated Model Extension

Hansen, C. E.; Kisslinger, J.; Krishna, N.; Holtzapple, E.; Ahmed, Y.; Miskov-Zivanov, N.

2021-10-01 systems biology
10.1101/2021.09.30.462421 bioRxiv
Show abstract

1In this study, we investigate the integration of three previously developed tools: FLUTE, VIOLIN, and CLARINET. We show how using these tools together adds additional capabilities in extending models from relevant research literature. We illustrate how we plan to address current modeling pitfalls with these tools (such as machine reading errors and literature volume), and how we plan to use these tools as the foundation for an automated model extension framework. Documentation and links to our tools can be found at: violin-tool.readthedocs.io clarinet-docs.readthedocs.io flute.readthedocs.io

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
BMC Bioinformatics
457 papers in training set
Top 0.2%
18.5%
2
Bioinformatics
1204 papers in training set
Top 2%
11.9%
3
Bioinformatics Advances
203 papers in training set
Top 0.2%
10.6%
4
Frontiers in Systems Biology
10 papers in training set
Top 0.1%
6.2%
5
Computational and Structural Biotechnology Journal
242 papers in training set
Top 0.5%
5.5%
50% of probability mass above
6
PLOS Computational Biology
1863 papers in training set
Top 7%
5.2%
7
PLOS ONE
5266 papers in training set
Top 31%
4.8%
8
Scientific Reports
3612 papers in training set
Top 42%
2.4%
9
BMC Research Notes
33 papers in training set
Top 0.3%
1.9%
10
Neuroinformatics
46 papers in training set
Top 0.5%
1.7%
11
Journal of Biomedical Informatics
47 papers in training set
Top 0.7%
1.7%
12
GigaScience
212 papers in training set
Top 2%
1.7%
13
Computers in Biology and Medicine
128 papers in training set
Top 2%
1.7%
14
Computer Methods and Programs in Biomedicine
28 papers in training set
Top 0.5%
1.7%
15
BioData Mining
22 papers in training set
Top 0.3%
1.7%
16
IEEE/ACM Transactions on Computational Biology and Bioinformatics
38 papers in training set
Top 0.6%
1.5%
17
Journal of Molecular Biology
232 papers in training set
Top 3%
1.1%
18
iScience
1154 papers in training set
Top 26%
1.1%
19
Database
61 papers in training set
Top 0.7%
1.1%
20
Briefings in Bioinformatics
354 papers in training set
Top 6%
1.1%
21
Biomolecules
100 papers in training set
Top 2%
0.9%
22
Journal of the American Medical Informatics Association
71 papers in training set
Top 2%
0.8%
23
Gigabyte
62 papers in training set
Top 1%
0.8%
24
BMC Medical Informatics and Decision Making
43 papers in training set
Top 2%
0.8%
25
Frontiers in Bioinformatics
49 papers in training set
Top 2%
0.6%
26
JAMIA Open
42 papers in training set
Top 2%
0.6%
27
Heliyon
152 papers in training set
Top 9%
0.6%
28
Frontiers in Artificial Intelligence
20 papers in training set
Top 1.0%
0.6%
29
Frontiers in Molecular Biosciences
102 papers in training set
Top 3%
0.6%
30
ACS Omega
105 papers in training set
Top 4%
0.6%