Harmonizome 3.0: Integrated knowledge about genes and proteins from diverse multi-omics resources
Nucleic Acids Research, ISSN: 1362-4962, Vol: 53, Issue: D1, Page: D1016-D1028
2025
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Article Description
By processing and abstracting diverse omics datasets into associations between genes and their attributes, the Harmonizome database enables researchers to explore and integrate knowledge about human genes from many central omics resources. Here, we introduce Harmonizome 3.0, a significant upgrade to the original Harmonizome database. The upgrade adds 26 datasets that contribute nearly 12 million associations between genes and various attribute types such as cells and tissues, diseases, and pathways. The upgrade has a dataset crossing feature to identify gene modules that are shared across datasets. To further explain significantly high gene set overlap between dataset pairs, a large language model (LLM) composes a paragraph that speculates about the reasons behind the high overlap. The upgrade also adds more data formats and visualization options. Datasets are downloadable as knowledge graph (KG) assertions and visualized with Uniform Manifold Approximation and Projection (UMAP) plots. The KG assertions can be explored via a user interface that visualizes gene-Attribute associations as ball-And-stick diagrams. Overall, Harmonizome 3.0 is a rich resource of processed omics datasets that are provided in several AI-ready formats. Harmonizome 3.0 is available at https://maayanlab.cloud/Harmonizome/.
Bibliographic Details
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85214585404&origin=inward; http://dx.doi.org/10.1093/nar/gkae1080; http://www.ncbi.nlm.nih.gov/pubmed/39565209; https://academic.oup.com/nar/article/53/D1/D1016/7905315; https://dx.doi.org/10.1093/nar/gkae1080; https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1080/7905315
Oxford University Press (OUP)
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