re: rebuilding knowledgebases (in nathalie's original post) it's good to want, but it's going to be hard as hell and we have to acknowledge that while they're not happening overnight, that's still no excuse for people to run to the robot.
November 12, 2026 at 5:55 PM
re: rebuilding knowledgebases (in nathalie's original post) it's good to want, but it's going to be hard as hell and we have to acknowledge that while they're not happening overnight, that's still no excuse for people to run to the robot.
Blog post on the article by Valerie Wood et al on the perilous stability of knowledgebases that form a core piece of the scientific infrastructure: genestogenomes.org/science-buil...
#Biocuration
#Biocuration
Science builds on science, but the databases making that possible are at risk
Scientific discoveries rarely happen in isolation. A finding from one laboratory can inspire an experiment in another, while an observation buried in a decades-old paper might provide the missing piec...
genestogenomes.org
November 6, 2026 at 8:15 PM
Blog post on the article by Valerie Wood et al on the perilous stability of knowledgebases that form a core piece of the scientific infrastructure: genestogenomes.org/science-buil...
#Biocuration
#Biocuration
From @rmazumde.bsky.social and colleagues in #OUP 's #DATABASE journal | Exploring protein #Glycosylation across GlyGen, UniProtKB, and related knowledgebases for data integration | #OpenScience #BioCuration #Proteomics #Carbohydrates CC/ @ebi.embl.org | 🧬🖥️🧪🔓
⬇️
academic.oup.com/database/art...
⬇️
academic.oup.com/database/art...
Exploring protein glycosylation across GlyGen, UniProtKB, and related knowledgebases for data integration
Abstract. Protein glycosylation plays a crucial role in cellular function, protein stability, and disease mechanisms, making the accurate annotation and in
academic.oup.com
October 30, 2026 at 5:58 PM
From @rmazumde.bsky.social and colleagues in #OUP 's #DATABASE journal | Exploring protein #Glycosylation across GlyGen, UniProtKB, and related knowledgebases for data integration | #OpenScience #BioCuration #Proteomics #Carbohydrates CC/ @ebi.embl.org | 🧬🖥️🧪🔓
⬇️
academic.oup.com/database/art...
⬇️
academic.oup.com/database/art...
Invisible infrastructure at risk: funding crises threaten global bioscience research academic.oup.com/genetics/art... #biocuration #databases #knowledgebases
Invisible infrastructure at risk: funding crises threaten global bioscience research
Abstract. Modern biology depends on invisible infrastructure that is essential yet precariously funded. Millions of biological observations are interpreted
academic.oup.com
October 27, 2026 at 4:37 PM
Invisible infrastructure at risk: funding crises threaten global bioscience research academic.oup.com/genetics/art... #biocuration #databases #knowledgebases
I have iidx data fully working on tumbleweed lol, with the kind of findings that I should probably post to the couple of knowledgebases pertaining to running these things on linux
this took a lot of doing and shots in the dark
this took a lot of doing and shots in the dark
October 11, 2026 at 2:49 AM
I have iidx data fully working on tumbleweed lol, with the kind of findings that I should probably post to the couple of knowledgebases pertaining to running these things on linux
this took a lot of doing and shots in the dark
this took a lot of doing and shots in the dark
Build a conversational claims assistant on Amazon Bedrock Knowledge Bases that answers natural-language questions from S3 documents with…
#Bedrock #KnowledgeBases #ClaimsAI #AWS
https://aws.amazon.com/blogs/machine-learning/query-claims-in-natural-language-with-amazon-bedrock-knowledge-bases/
#Bedrock #KnowledgeBases #ClaimsAI #AWS
https://aws.amazon.com/blogs/machine-learning/query-claims-in-natural-language-with-amazon-bedrock-knowledge-bases/
October 3, 2026 at 10:00 AM
Build a conversational claims assistant on Amazon Bedrock Knowledge Bases that answers natural-language questions from S3 documents with…
#Bedrock #KnowledgeBases #ClaimsAI #AWS
https://aws.amazon.com/blogs/machine-learning/query-claims-in-natural-language-with-amazon-bedrock-knowledge-bases/
#Bedrock #KnowledgeBases #ClaimsAI #AWS
https://aws.amazon.com/blogs/machine-learning/query-claims-in-natural-language-with-amazon-bedrock-knowledge-bases/
You should tell every lab that is spending money on bespoke solutions to this that they’re all wrong for building knowledgebases, I’m sure it’ll go over great
September 17, 2026 at 3:20 PM
You should tell every lab that is spending money on bespoke solutions to this that they’re all wrong for building knowledgebases, I’m sure it’ll go over great
The difference is usually in whether you're likable or not.
Nerds are cool
Geeks are to be avoided
Even when their individual fixations/knowledgebases are the same thing.
Nerds are cool
Geeks are to be avoided
Even when their individual fixations/knowledgebases are the same thing.
What is the difference between a nerd and a geek?
I feel like these terms have gotten conflated
I feel like these terms have gotten conflated
September 8, 2026 at 4:27 PM
The difference is usually in whether you're likable or not.
Nerds are cool
Geeks are to be avoided
Even when their individual fixations/knowledgebases are the same thing.
Nerds are cool
Geeks are to be avoided
Even when their individual fixations/knowledgebases are the same thing.
So when people talk about how it makes software so much easier, they have made the mechanical part much easier with basically super grep - massively applying SWEBOK and Stack Overflow and all the tech support knowledgebases into making basic coding very much faster. Because all this is NOT novel.
September 8, 2026 at 4:01 AM
So when people talk about how it makes software so much easier, they have made the mechanical part much easier with basically super grep - massively applying SWEBOK and Stack Overflow and all the tech support knowledgebases into making basic coding very much faster. Because all this is NOT novel.
✍️ New blog post by Gerardo Arroyo
I Took the Wheel Off My RAG: Managed KB vs. Manual Chunking
#aws #bedrock #agentcore #knowledgebases
I Took the Wheel Off My RAG: Managed KB vs. Manual Chunking
#aws #bedrock #agentcore #knowledgebases
I Took the Wheel Off My RAG: Managed KB vs. Manual Chunking
In April I published a benchmark comparing 5 chunking strategies in Amazon Bedrock Knowledge Bases....
dev.to
September 4, 2026 at 1:44 PM
✍️ New blog post by Gerardo Arroyo
I Took the Wheel Off My RAG: Managed KB vs. Manual Chunking
#aws #bedrock #agentcore #knowledgebases
I Took the Wheel Off My RAG: Managed KB vs. Manual Chunking
#aws #bedrock #agentcore #knowledgebases
Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings
Susanna Bravi et al.
#arXiv #cs.AI
Susanna Bravi et al.
#arXiv #cs.AI
Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings
Biological knowledgebases like Reactome provide high-quality pathways that include biological elements' relationships and textual descriptions (metadata). The quality of such pathways is granted by manual curation, that presents, however, significant scalability challenges. Lately, numerous NLP too…
arxiv.org
September 1, 2026 at 11:25 PM
Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings
Susanna Bravi et al.
#arXiv #cs.AI
Susanna Bravi et al.
#arXiv #cs.AI
Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings
Biological knowledgebases like Reactome provide high-quality pathways that include biological elements' relationships and textual descriptions (metadata). The quality of such pathways is granted by manual curation, that presents, however, significant scalability challenges. Lately, numerous NLP too…
arxiv.org
August 31, 2026 at 11:28 PM
Joking aside, how do you get a complete dogma shift that requires a rewriting of all of our interaction/etc. knowledgebases?
August 29, 2026 at 9:58 PM
Joking aside, how do you get a complete dogma shift that requires a rewriting of all of our interaction/etc. knowledgebases?
recent times have made it clear how vital knowledgebases like FlyBase @flybase.bsky.social are to the scientific community. and that they are not simply static websites, but living, dynamic, active entities run by dedicated humans. they require continuous support and can't be taken for granted. 🪰
Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
Treat biological databases as infrastructure, not projects
Letter to the Editor
www.nature.com
August 20, 2026 at 12:57 PM
recent times have made it clear how vital knowledgebases like FlyBase @flybase.bsky.social are to the scientific community. and that they are not simply static websites, but living, dynamic, active entities run by dedicated humans. they require continuous support and can't be taken for granted. 🪰
getting together a lil band of gringos to practice speaking spanish together every week was such a good idea . we all have v different knowledgebases too so generally one of us can answer a question another has with 70% certainty relevant in at least one country LOL
September 17, 2024 at 12:11 AM
getting together a lil band of gringos to practice speaking spanish together every week was such a good idea . we all have v different knowledgebases too so generally one of us can answer a question another has with 70% certainty relevant in at least one country LOL
Yesterday, I added Karpathy's approach to my Obsidian vault and projects. Set up Claude Cowork to scan for content daily from Readwise and Snipd for updating the knowledgebases.⏩ 🧠 #pkm #para #secondbrain
April 15, 2026 at 6:50 PM
Yesterday, I added Karpathy's approach to my Obsidian vault and projects. Set up Claude Cowork to scan for content daily from Readwise and Snipd for updating the knowledgebases.⏩ 🧠 #pkm #para #secondbrain
@tomjennings
In addition to allowing people to cooperate asynchronously, which can be very important for people in diverse timezones, things like Discourse or NodeBB have been successful as sort of knowledgebases you can search. If people have questions about how to do things or whatever, if […]
In addition to allowing people to cooperate asynchronously, which can be very important for people in diverse timezones, things like Discourse or NodeBB have been successful as sort of knowledgebases you can search. If people have questions about how to do things or whatever, if […]
Original post on mastodon.sdf.org
mastodon.sdf.org
March 19, 2026 at 5:15 AM
@tomjennings
In addition to allowing people to cooperate asynchronously, which can be very important for people in diverse timezones, things like Discourse or NodeBB have been successful as sort of knowledgebases you can search. If people have questions about how to do things or whatever, if […]
In addition to allowing people to cooperate asynchronously, which can be very important for people in diverse timezones, things like Discourse or NodeBB have been successful as sort of knowledgebases you can search. If people have questions about how to do things or whatever, if […]
Great work and an ingenious application of the UniProt and @rhea-db.bsky.social knowledgebases!
October 27, 2025 at 10:06 AM
Great work and an ingenious application of the UniProt and @rhea-db.bsky.social knowledgebases!
AD: Examples of variants in somatic knowledgebases: "c dot" (frameshift, splice donor), "p dot" (missense), categorical bucket variants #ACMGMtg24
March 15, 2024 at 8:09 PM
AD: Examples of variants in somatic knowledgebases: "c dot" (frameshift, splice donor), "p dot" (missense), categorical bucket variants #ACMGMtg24
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation url: academic.oup.com/bioinformati... @elixiruknode.org @biocurator.bsky.social
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation
Abstract. Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable f
academic.oup.com
February 16, 2026 at 8:18 AM
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation url: academic.oup.com/bioinformati... @elixiruknode.org @biocurator.bsky.social
I do think a lot of us will eventually get *there* and get *it* but we're definitely on different tracks and have different resources and knowledgebases.
I am so grateful for those people from the left who were highly critical of Obama before I could get there or get it. I eventually did, though.
I am so grateful for those people from the left who were highly critical of Obama before I could get there or get it. I eventually did, though.
October 19, 2025 at 1:27 AM
I do think a lot of us will eventually get *there* and get *it* but we're definitely on different tracks and have different resources and knowledgebases.
I am so grateful for those people from the left who were highly critical of Obama before I could get there or get it. I eventually did, though.
I am so grateful for those people from the left who were highly critical of Obama before I could get there or get it. I eventually did, though.
🔗 Developing foundations for biomedical knowledgebases from literature using large language models – A systematic assessment. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs...
📚 CSBJ: www.csbj.org
#LargeLanguageModels #BiomedicalAI #DigitalHealth #Bioinformatics #LLM
📚 CSBJ: www.csbj.org
#LargeLanguageModels #BiomedicalAI #DigitalHealth #Bioinformatics #LLM
September 2, 2025 at 10:17 PM
🔗 Developing foundations for biomedical knowledgebases from literature using large language models – A systematic assessment. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs...
📚 CSBJ: www.csbj.org
#LargeLanguageModels #BiomedicalAI #DigitalHealth #Bioinformatics #LLM
📚 CSBJ: www.csbj.org
#LargeLanguageModels #BiomedicalAI #DigitalHealth #Bioinformatics #LLM
🚀 Product Hunt Daily — Thursday, July 23, 2026
#1 Teable 3.0 · #2 PodcastorAI · #3 CrawlRaven · #4 PromptQL · #5 Moxie Docs: Knowledgebases
#ProductHunt #Startups #Tech
#1 Teable 3.0 · #2 PodcastorAI · #3 CrawlRaven · #4 PromptQL · #5 Moxie Docs: Knowledgebases
#ProductHunt #Startups #Tech
July 23, 2026 at 12:00 PM
🚀 Product Hunt Daily — Thursday, July 23, 2026
#1 Teable 3.0 · #2 PodcastorAI · #3 CrawlRaven · #4 PromptQL · #5 Moxie Docs: Knowledgebases
#ProductHunt #Startups #Tech
#1 Teable 3.0 · #2 PodcastorAI · #3 CrawlRaven · #4 PromptQL · #5 Moxie Docs: Knowledgebases
#ProductHunt #Startups #Tech
Chemical representation standardization needed to generalize metabolic pathway involvement prediction across the Kyoto Encyclopedia of Genes and Genomes, Reactome, and MetaCyc knowledgebases https://www.biorxiv.org/content/10.1101/2025.04.02.646918v1
April 8, 2025 at 11:06 PM
Chemical representation standardization needed to generalize metabolic pathway involvement prediction across the Kyoto Encyclopedia of Genes and Genomes, Reactome, and MetaCyc knowledgebases https://www.biorxiv.org/content/10.1101/2025.04.02.646918v1
🐿 Feeling squirrely about #AI #agents? I have a new O'Reilly book coming out that might help! "Building Agentic Solutions with Microsoft Foundry" comes out in a few months, but you can read chapters 1-3 today!
🔗: www.oreilly.com/library/view...
#microsoftfoundry #azure #finetuning #knowledgebases 🌰
🔗: www.oreilly.com/library/view...
#microsoftfoundry #azure #finetuning #knowledgebases 🌰
March 3, 2026 at 7:28 PM
🐿 Feeling squirrely about #AI #agents? I have a new O'Reilly book coming out that might help! "Building Agentic Solutions with Microsoft Foundry" comes out in a few months, but you can read chapters 1-3 today!
🔗: www.oreilly.com/library/view...
#microsoftfoundry #azure #finetuning #knowledgebases 🌰
🔗: www.oreilly.com/library/view...
#microsoftfoundry #azure #finetuning #knowledgebases 🌰