Knowledge Pixels Incubator #5: A community-driven linked knowledge base for plant specialized metabolism
Project
📅 Date
ℹ About
Plant specialized metabolites are a major source of medicines, novel foods, and natural products, yet the knowledge needed to discover and characterize them remains scattered across publications, databases, and tools. This project uses nanopublications to build PlantMetWiki, a queryable, community-driven knowledge base that links experimentally characterized plant biosynthetic pathways with repositories such as PlantCyc, plantiSMASH, MIBiG, and LOTUS. By representing pathway data, multi-omics predictions, and community annotations as nanopublications, the knowledge base enables machine-readable sharing and continuous integration of new findings. Researchers will be able to query across experimental and predicted data to prioritize promising biosynthetic candidates for wet-lab validation, while contributing their own results back to the community as Linked Open Data.
Roles:
(none)
Admins
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Observers
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Project Leads
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📌 Relevant resources
- https://plantmetwiki.bioinformatics.nl/ PlantMetWiki SPARQL Explorer · https://w3id.org/np/RAcyENoff2... ^
- https://github.com/pathway-lod/ Pathway LOD GitHub Community · Pathway Linked Open Data: Linked Open Data for Pathway Information · https://w3id.org/np/RAXg-N4Ts8... ^
- https://zenodo.org/communities/plantmetwiki/ PlantMetWiki Zenodo community · Communities are shared areas on Zenodo where projects, institutions, domains, and conferences can curate and manage their research outputs. · https://w3id.org/np/RAeYxPVRge... ^
📢 Our news
- Workshop “Biosynthesis of Natural Products: From Genes to Molecules to Data · On Monday 20th April, I had the chance to present a flash talk at the workshop “Biosynthesis of Natural Products: From Genes to Molecules to Data” 🧬 In my talk 🔦 “Catalyzing Plant Natural Product Discovery with a Community-driven Linked Knowledge Base” 🔦, I presented 🌐🌱PlantMetWiki 🌐🌱 the first open, queryable platform to explore plant biosynthesis and biochemistry through linked open data. · 2026-04-22 · https://www.linkedin.com/posts...nAB8AzO_2Kcut1TTTktTQ_wG8u6ppQ elena-del-pup-840805164_plantmetwiki-fairdatafund-retromol-activity-7452646859216498688-c12C · https://w3id.org/np/RAOKW02Qly... ^
- Incubator project #5 · We are excited to announce that we are launching our fifth incubator project, A community-driven linked knowledge base for plant specialized metabolism, led by Elena Del Pup. · 2026-03-31 · https://w3id.org/np/RA_LQwciGN... ^
💬 Messages
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Elena introducing the topic of her incubator project right now at our office hour. I learned that plants are our best chemists! Super interesting :)
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2026-04-22T12:17:09.908Z
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It's great to have this incubator project. I'm looking forward to seeing what comes out of it :)
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2026-04-08T15:30:10.367Z
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