User benefits of #uniprot are estimated to be on the order of 20 times higher than operational costs https://www.sib.swiss/news/uniprot-user-benefits-up-to-39-times-higher-than-operational-costs
#UniProt
#UniProt The largest open+free #knowledgegraph in the life sciences. I will be talking about the why and the use cases at #semantics2025 5th of September 2025. Looking forward to seeing you all there!
https://2025-eu.semantics.cc/page/sessions?page=1nZsC6p2V3Yk73axR9Jl1NWq1IhVpkqtN
#Update! Version 10.5.0 is live.
Featuring increases in the number of #Research products and affiliations, as well as updated mapping to import BioEntities from #ProteinDataBank and #ResearchData from #UniProt.
See all updates in the changelog!
Changelog https://graph.openaire.eu/changelog
#ScholarlyKnowledgeGraph #ScientificKnowledgeGraph #SKG #OpenData #OpenScience
Interesting in his #ISMBECCB2025 keynote that Amos Bairoch described as the worst decision of his career: caving to USA pressure to switch from funding model of free to academics & non-profits to use #SwissProt / #UniProt (with no login barrier), but paid access to Industry - to a free-to-all model funded by an NIH grant.
[I suspect industry lobbying at NIH there. One issue with grants is they are typically fixed term. Also, this would have been a very strong precedent for other DBs to follow - would have been more sustainable ecosystem?]
#uniprot just hides the controls.. so you can't even try to full screen. but you can fortunately link out the #ebi #alphafold site where (ctd..)
🧬 How do AlphaFold2 and ESMFold stack up when it comes to functional annotation?
🔗 AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.01.008
📚 CSBJ: https://www.csbj.org/
#AlphaFold2 #ESMFold #AIinScience #ProteinStructure #Enzymes #Pfam #UniProt #AlphaFold #HumanProteome #FunctionalAnnotation #AIinBiology #ComputationalBiology #FunctionalGenomics
In 2023, ISB members voted to award Sandra Orchard the Exceptional Contribution to Biocuration award (https://www.biocuration.org/pascale-gaudet-and-sandra-orchard-recipients-of-the-2023-exceptional-contribution-to-biocuration-award).
Today at #biocuration2025 in Kansas City, she's presenting her award talk "How will the role of the Biocurator change in this world of Artificial Intelligence and Machine-Learning?" with a focus on current work at UniProt
At @swat4hcls there was a presentation by @albdrg that I really like: https://www.youtube.com/watch?v=F4Nl-nmLZA4 This uses #SPARQL to combine data in a privacy aware #beacons-api and combine it with public #knowledgegraph like #uniprot by @SIB and #wikidata @wikidata to reduce cost of the data integration challenge required to answer clinical question.
Slide from my talk "Open Science for Medicine and Society" at Komazawa university. Using GNU Health to select a BRCA1 variant involved in breast #cancer and the 3D representation of the BRCT domain using PyMOL.
Having access to the latest scientific evidence makes a huge difference in patients, yet medical research is being dismantled by #corporatocracy.
Medicine and society evolves not because of the bullshit hype of AI, but because of the effort and talent of the men and women behind these projects. Respect :anarchoheart3: 🩺
#UniProt #HUGO #GNUHealth #PyMOL #NIH #genomics #OpenScience
My #SPARQL query of the day: List all known organisms in the #uniprot taxonomy database for which the donor of a sample depicted in #OMERO
is a host. Promptly answered
by federating local #OMERO Virtual Knowledge Graph and https://sparql.uniprot.org/sparql. I love it. CC: @nfdi4bioimage @joshmoore #NFDIrocks.
a bit over 17 years ago: "One Billion Biochemical RDF Triples!" https://chem-bla-ics.linkedchemistry.info/2007/10/24/one-billion-biochemical-rdf-triples.html
More cool entity descriptions amplified by <#LinkedData> pages: #HCLS #Uniprot #SemanticWeb #NewSQL #BigData
Virtuoso Column Store Edition #BSBM and #Uniprot benchmark numbers: . #DBMS #LinkedData #SPARQL #BigData #SemanticWeb
Post frm Orri Erling (#virtuoso prg. mgr) re. #RDF data loader enhancements & its effect on #DBpedia, #Uniprot loading: http://bit.ly/dwOTML
Very honored by the kind acknowledgements in https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae959/7848838 by @ju I am very existed about doing cross database queries between #uniprot #rhea and media data in #bacdive @dsmz
If the protein or complex was purified from its native host organism:
1. I sequence the map with `model_angelo build_no_seq`.
2. I identify all proteins with `model_angelo hmm_search` against the reference proteome of the host organism (downloaded from #Uniprot).
If the protein or complex was prepared recombinantly, I already know the sequences of all proteins.
So at this stage, either way, I know which proteins are in there.
3/19
With we I actually mean: you the #UniProt user base ;)
#DidYouKnow that institutions are using #GNUHealth for the diagnostic and management of #genetic diseases? In addition, and thanks to our friends from #uniprot we provide the large human natural variants dataset & related conditions.
Check out the genetics chapter from our official documentation for more information about #genomics and medical genetics 👇
https://docs.gnuhealth.org/his/userguide/modules/genetics.html
Moving forward with #OpenScience ♥️ 🧬
#PrecisionMedicine
Looking forward to talk about #FAIR #UniProt and #SPARQL later today https://cost-dkg.eu/talks#UniProt%20and%20others:%20FAIRly%20large%20and%20connected%20SPARQL%20in%20the%20life-sciences
Missed the course on #Enzymes in #UniProt yesterday. Rest assured, the presentation will be available on the @SIB youtube channel soon (https://www.youtube.com/@sib-swissinstituteofbioinf4579). The course materials are already available at https://education.expasy.org/cours/SIB_UniProtKB_Enzymes_2024/
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