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BioMedTools: a language model-powered community for biomedical computational tools

Liu, S.; Xing, H.; Han, M.; Zhang, D.; Gong, L.; Liu, D.; Chen, J.; Cai, P.; Hu, Q.-N.

2025-05-08 bioinformatics
10.1101/2025.05.02.651919 bioRxiv
Show abstract

A large number of biomedical computational tools have spawned several tool registries. However, in the face of the rapid growth in the number of tools, existing tool registries, which are manually curated or community-driven, are difficult to keep up to date, resulting in inadequate tool repository data. In this paper, we show that language models (LMs) can aid in building a community of tools. We introduce BioMedTools (https://biomed.tools), a community of biomedical computational tools that mainly implements LM-based tool identification and a chat assistant. Compared with existing tool registries, BioMedTools achieves excellence in terms of the number of tools, frequency of data updates, and functionality. Meanwhile, the Model Context Protocol (MCP) servers hub in BioMedTools may promote the building of agents in the biomedical field. BioMedTools enables the efficient collection of tools and enhances their findability and accessibility.

Matching journals

The top 6 journals account for 50% of the predicted probability mass.

1
Database
◐ 61 papers in training set
Top 0.1%
11.6%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 2%
11.6%
Similar papers in this journal
3
Briefings in Bioinformatics
◐ 354 papers in training set
Top 0.7%
9.5%
Similar papers in this journal
4
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 0.4%
6.5%
Similar papers in this journal
5
Genomics, Proteomics & Bioinformatics
188 papers in training set
Top 0.3%
6.1%
6
GigaScience
◐ 212 papers in training set
Top 0.4%
6.1%
50% of probability mass above
7
BMC Bioinformatics
○ 457 papers in training set
Top 2%
5.0%
8
Scientific Reports
○ 3612 papers in training set
Top 27%
3.9%
9
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.9%
10
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 1%
3.4%
11
Nucleic Acids Research
◐ 1281 papers in training set
Top 6%
3.1%
12
Scientific Data
○ 209 papers in training set
Top 1%
2.3%
13
Patterns
○ 78 papers in training set
Top 1%
1.9%
14
BioData Mining
○ 22 papers in training set
Top 0.2%
1.7%
15
Computers in Biology and Medicine
○ 128 papers in training set
Top 3%
1.5%
16
iScience
○ 1154 papers in training set
Top 22%
1.5%
17
Genome Biology
○ 637 papers in training set
Top 7%
1.3%
18
PLOS Computational Biology
● 1863 papers in training set
Top 18%
1.0%
19
Journal of Biomedical Informatics
○ 47 papers in training set
Top 1%
1.0%
20
F1000Research
○ 88 papers in training set
Top 3%
1.0%
21
Nature Communications
○ 5641 papers in training set
Top 54%
0.9%
22
Journal of the American Medical Informatics Association
◐ 71 papers in training set
Top 2%
0.8%
23
eLife
● 5828 papers in training set
Top 68%
0.8%
24
PLOS ONE
● 5266 papers in training set
Top 63%
0.6%
25
iMeta
○ 10 papers in training set
Top 0.3%
0.6%
26
IEEE/ACM Transactions on Computational Biology and Bioinformatics
● 38 papers in training set
Top 1%
0.6%
27
Journal of Molecular Biology
○ 232 papers in training set
Top 5%
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.