ArticleNucleic acids research2022
ProteomicsDB: toward a FAIR open-source resource for life-science research.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
44 citing papers in PubMed.
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- Chondrogenic potential of mesenchymal progenitors from somatic and cartilage-derived iPSCs is predicted by their transcriptomic signatures.Genes & diseases · 2026Article
- Exploring and expanding the chemical multiverse of peptides.Chemical science · 2026Review
- Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.Nucleic acids research · 2026Article
- PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.Nucleic acids research · 2026Article
- MouseOmics: a multi-omics database for mouse biological study.Nucleic acids research · 2026Article
- OmicsQ: a user-friendly platform for interactive quantitative omics data analysis.Bioinformatics (Oxford, England) · 2026Article
- Computational design and evaluation of optimal bait sets for scalable proximity proteomics.Nature communications · 2025Article
- Integrative Multi-Omics Characterization and Structural Insights into the Poorly Annotated IntegrinGenes · 2025Article
- In vivo and in silico models of Drosophila for Parkinson's disease.The FEBS journal · 2025Review
- Genome-wide association study for lung cancer in 6531 African Americans reveals new susceptibility loci.Human molecular genetics · 2025Article
- Serendipitous and Systematic Chemoproteomic Discovery of MBLAC2, HINT1, and NME1-4 Inhibitors from Histone Deacetylase-Targeting Pharmacophores.ACS chemical biology · 2025Article
- A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.Journal of proteome research · 2025Article
- Protein subinteractomes of human microsomal cytochromes P450.Molecular biology reports · 2025Review
- PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.Nature communications · 2025Article
- AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships.Computational and structural biotechnology journal · 2025Review
- Decision Tree for Protein Biomarker Selection for Clinical Applications.Methods in molecular biology (Clifton, N.J.) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.