PubMed gene/cell type-relation Atlas (PuMA)

Please cite the following paper:

Plain

Lucas Bickmann, Sarah Sandmann, Carolin Walter, Julian Varghese
PuMA: PubMed gene/cell type-relation Atlas.
BMC Bioinformatics 26, 201 (2025). https://doi.org/10.1186/s12859-025-06236-8

Bibtex

@article{bickmann_puma_2025,
title = {{PuMA}: {PubMed} gene/cell type-relation {Atlas}},
volume = {26},
issn = {1471-2105},
url = {https://doi.org/10.1186/s12859-025-06236-8},
doi = {10.1186/s12859-025-06236-8},
number = {1},
journal = {BMC Bioinformatics},
author = {Bickmann, Lucas and Sandmann, Sarah and Walter, Carolin and Varghese, Julian},
month = jul,
year = {2025},
pages = {201},
}

How to:

1. Select the appropriate navigation element (Genes, Cells, Graphs).
2. Enter the search term
3. Select if you want an exact match and a filter for the minimal score/number of nodes (for Graphs)
4. Press Search

You can filter, sort and export the results with the appropiate described element. The graph view allows interactions.

Score information:

There exists two metrics: #PubMedIDs and #Occurences.
#PubMedIDs is the number where at least one occurence for the specific CUI is made.
#Occurence is the number of occurence for all PubMedIDs.

PuMA uses the following scoring scheme:
score = log₁₀(#PubMedIDs) * log₁₀(#Occurences)
The additional log-scaling is applied to filter extremly high expressed mentions and occurences.