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FAIRification of computational models in biology

Balaur, I.; Nickerson, D. P.; Welter, D.; Wodke, J. A. H.; Ancien, F.; Gebhardt, T.; Groues, V.; Hermjakob, H.; Konig, M.; Radde, N.; Rougny, A.; Schneider, R.; Malik Sheriff, R. S.; Shiferaw, K. B.; Stefan, M.; Satagopam, V. P.; Waltemath, D.

2025-03-24 systems biology
10.1101/2025.03.21.644517 bioRxiv
Show abstract

Computational models are essential for studying complex systems which, particularly in clinical settings, need to be quality-approved and transparent. To enhance the communication of a models features and capabilities, we propose an adaptation of the Findability, Accessibility, Interoperability and Reusability (FAIR) indicators published by the Research Data Alliance to assess models encoded in domain-specific standards, such as those established by COMBINE. The assessments guide FAIRification and add value to models.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
Scientific Data
○ 209 papers in training set
Top 0.1%
37.7%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 3%
6.9%
Similar papers in this journal
3
GigaScience
◐ 212 papers in training set
Top 0.7%
4.6%
Similar papers in this journal
4
PLOS Computational Biology
● 1863 papers in training set
Top 9%
3.4%
Similar papers in this journal
50% of probability mass above
5
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 1%
3.3%
Similar papers in this journal
6
iScience
○ 1154 papers in training set
Top 8%
3.1%
7
Nucleic Acids Research
◐ 1281 papers in training set
Top 6%
3.1%
8
Scientific Reports
○ 3612 papers in training set
Top 39%
2.5%
9
Nature Communications
○ 5641 papers in training set
Top 40%
2.3%
10
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.0%
11
npj Systems Biology and Applications
○ 125 papers in training set
Top 0.8%
2.0%
12
Nature Protocols
○ 33 papers in training set
Top 0.2%
2.0%
13
PLOS ONE
● 5266 papers in training set
Top 45%
1.8%
14
Database
◐ 61 papers in training set
Top 0.5%
1.6%
15
Genome Biology
○ 637 papers in training set
Top 6%
1.6%
16
Patterns
○ 78 papers in training set
Top 2%
1.4%
17
eLife
● 5828 papers in training set
Top 55%
1.4%
18
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.4%
19
Cell Reports Methods
○ 165 papers in training set
Top 2%
1.4%
20
Frontiers in Bioinformatics
○ 49 papers in training set
Top 0.7%
1.3%
21
Bioinformatics Advances
◐ 203 papers in training set
Top 4%
1.1%
22
Journal of Molecular Biology
○ 232 papers in training set
Top 3%
1.1%
23
Frontiers in Physiology
○ 106 papers in training set
Top 2%
1.0%
24
International Journal of Molecular Sciences
○ 494 papers in training set
Top 13%
1.0%
25
Molecular Systems Biology
○ 162 papers in training set
Top 3%
1.0%
26
Frontiers in Bioengineering and Biotechnology
○ 98 papers in training set
Top 3%
0.8%
27
Neuroinformatics
○ 46 papers in training set
Top 0.9%
0.8%
28
Frontiers in Systems Biology
○ 10 papers in training set
Top 0.2%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.