#uniprot — Public Fediverse posts

To our government officials: Please invest our tax money in science, not in stupid wars.

Let me explain... while Python is keeping busy my laptop doing number crunching, I thought I'd share with you part of process of updating GNU Health HIS genomic packages to the latest genes, symbols, human natural variants and their phenotypes / diseases for 2026. Quite a lot of work, for the betterment of the society, ad honorem.

So again to all in @EUCommission, instead of putting millions of euros in weapons and in the macabre business of war, invest in science, education and healthcare. Thank you.

#OpenScience #GNUHealth #GNU #bioinformatics #genomics #HUGO #UniProt #genetics #health #PublicHealth

My Domain: proteome-wide scanning of TMDs

https://quantixed.org/2026/04/16/my-domain-proteome-wide-scanning-of-tmds/

#science #bioinformatics #CellBiology #proteins #Rstats #Uniprot

My Domain: proteome-wide scanning of TMDs

https://quantixed.org/2026/04/16/my-domain-proteome-wide-scanning-of-tmds/

#science #bioinformatics #CellBiology #proteins #Rstats #Uniprot

My Domain: proteome-wide scanning of TMDs

https://quantixed.org/2026/04/16/my-domain-proteome-wide-scanning-of-tmds/

#science #bioinformatics #CellBiology #proteins #Rstats #Uniprot

My Domain: proteome-wide scanning of TMDs

https://quantixed.org/2026/04/16/my-domain-proteome-wide-scanning-of-tmds/

#science #bioinformatics #CellBiology #proteins #Rstats #Uniprot

My Domain: proteome-wide scanning of TMDs

https://quantixed.org/2026/04/16/my-domain-proteome-wide-scanning-of-tmds/

#science #bioinformatics #CellBiology #proteins #Rstats #Uniprot

Love how https://consensus.rubalkhali.science/ links ecological data to the molecular world of #UniProt with some smarts and the power of federated #SPARQL

@harmonia_amanda the vast majority of #SPARQL experts are autodidact! Heck I learn more from the #uniprot sparql endpoint users with their user cases than from the language spec. The joy of seeing smart scientist play with the data is amazing

https://www.europesays.com/ie/198966/ AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions | BMC Bioinformatics #algorithms #AlphaFoldDB #APIToolkit #Bioinformatics #ComputationalBiology #ComputationalBiology/Bioinformatics #ComputerAppl.InLifeSciences #Éire #IE #Ireland #Microarrays #NCBI #OpenAccess #ProteinStructure #Science #StructuralGenomics #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

#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

#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

#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

#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

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

#biocuration #uniprot #mods #proteins #complexportal

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.

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

I am looking for an #ontology #schema that I can use to mark up where #sparql example is known to work. e.g. a query that works for #uniprot and #bgee or #omabrowser. Please share for reach.

**Problem:**
#LLM based #SmartAgent solutions like #ChatGPT are fantastic natural language processors, but challenged by unpredictable guessing.

**Solution:**
Fine-tune using #SPARQL query templates and a #LODCloud #KnowledgeGraph like @Uniprot.

https://community.openlinksw.com/t/using-sparql-query-templates-to-fine-tune-chatgpts-large-language-model-llm/3842/5#uniprot-knowledge-graph-chatgpt-fine-tuning-using-sparql-1

#SemanticWeb #LinkedData #HowTo #LLMs #Uniprot #Bioinformatics #Genomics #MolecularBiology #LifeSciences

Applications session: Talk

3. Elisabeth Coudert talks about Annotation of biologically relevant ligands - such as substrates of enzymes, cofactors, activators, inhibitors as well as their binding site - in UniProt using ChEBI

#biocuration2023 #Applications #uniprot #chebi

#SIB Preprint on the power and limitations of #AI #chatbots such as #chatgpt to understand #SPARQL federated queries over #UniProt, #OMA and #Bgee https://arxiv.org/abs/2304.10427

For many years I've observed the following in parallel:

1. General confusion (and in some cases disdain) about the notion of a #SemanticWeb

2. Steadfast effort by a community to keep the vision going, stealthily, as exemplified by the #LODCloud (#DBpedia,, #Wikidata, #Uniprot etc..) and Schema.org (#SchemaOrg)

3. #DataSilos and all the impedance they inflict on the agility of individuals and enterprises alike on the rise i.e., #DataAccess and #DataFlow are still challenging, unnecessarily.

For many years I've observed the following in parallel:

1. General confusion (and in some cases disdain) about the notion of a #SemanticWeb

2. Steadfast effort by a community to keep the vision going, stealthily, as exemplified by the #LODCloud (#DBpedia,, #Wikidata, #Uniprot etc..) and Schema.org (#SchemaOrg)

3. #DataSilos and all the impedance they inflict on the agility of individuals and enterprises alike on the rise i.e., #DataAccess and #DataFlow are still challenging, unnecessarily.

For many years I've observed the following in parallel:

1. General confusion (and in some cases disdain) about the notion of a #SemanticWeb

2. Steadfast effort by a community to keep the vision going, stealthily, as exemplified by the #LODCloud (#DBpedia,, #Wikidata, #Uniprot etc..) and Schema.org (#SchemaOrg)

3. #DataSilos and all the impedance they inflict on the agility of individuals and enterprises alike on the rise i.e., #DataAccess and #DataFlow are still challenging, unnecessarily.

For many years I've observed the following in parallel:

1. General confusion (and in some cases disdain) about the notion of a #SemanticWeb

2. Steadfast effort by a community to keep the vision going, stealthily, as exemplified by the #LODCloud (#DBpedia,, #Wikidata, #Uniprot etc..) and Schema.org (#SchemaOrg)

3. #DataSilos and all the impedance they inflict on the agility of individuals and enterprises alike on the rise i.e., #DataAccess and #DataFlow are still challenging, unnecessarily.

For many years I've observed the following in parallel:

1. General confusion (and in some cases disdain) about the notion of a #SemanticWeb

2. Steadfast effort by a community to keep the vision going, stealthily, as exemplified by the #LODCloud (#DBpedia,, #Wikidata, #Uniprot etc..) and Schema.org (#SchemaOrg)

3. #DataSilos and all the impedance they inflict on the agility of individuals and enterprises alike on the rise i.e., #DataAccess and #DataFlow are still challenging, unnecessarily.

MyGNUhealth, the GNU Health Personal Health Record 1.0.3 is out! Updates the medical #genetics w/ the latest #UniProt human natural variants.
Ready for your desktop, and your @thepine64 #PinePhone ❤️ #bioinformatics #PHR #mhealth 👇
savannah.gnu.org/forum/forum.ph…