FAIR DATA Fund use case: Catalyzing plant natural product discovery with a community-driven knowledge base

Authors: Ele­na Del Pup (4th edi­tion FAIR Data Fund grantee); Justin J. J. van der Hooft, Marnix H. Mede­ma; Wagenin­gen Uni­ver­si­ty & Research. Edi­tor: Iulia Popes­cu

Plants spe­cial­ized metab­o­lism is a major source of med­i­cines, nov­el foods, and nat­ur­al prod­ucts. With the rapid growth of mul­ti-omics data and paired plant transcriptomics–metabolomics datasets, there are unprece­dent­ed oppor­tu­ni­ties to uncov­er the biosyn­thet­ic steps for the pro­duc­tion of these mol­e­cules. How­ev­er, sys­tem­at­ic explo­ration of this data remains prob­lem­at­ic because infor­ma­tion about plant chem­istry, biosyn­the­sis, and exper­i­men­tal data is scat­tered across indi­vid­ual datasets and pub­li­ca­tions, mak­ing it dif­fi­cult to lever­age it for pre­dic­tions and AI meth­ods.

In this project, we are build­ing a linked, queryable knowl­edge base that inte­grates paired mul­ti-omics, curat­ed path­way knowl­edge, and com­mu­ni­ty anno­ta­tions. To achieve this, we are build­ing Plant Wikipath­ways, a queryable knowl­edge base of exper­i­men­tal­ly char­ac­ter­ized plant path­ways, by link­ing it to repos­i­to­ries across biosyn­the­sis. Users will be able to query across exper­i­men­tal and pub­lic data to extract promis­ing path­way pre­dic­tions allow­ing for fur­ther val­i­da­tion. The com­pu­ta­tion­al strate­gies and tools devel­oped in this project will sup­port a com­mu­nal effort to facil­i­tate large-scale and repro­ducible analy­sis of plant meta­bol­ic diver­si­ty and nat­ur­al prod­uct biosyn­the­sis, extend­ing on approach­es for life sci­ences such as Wiki­da­ta. This open-source knowl­edge base will serve as a Linked Open Data com­mu­ni­ty for col­lab­o­ra­tive hypoth­e­sis gen­er­a­tion on plant spe­cial­ized biosyn­the­sis, pri­or­i­ti­za­tion of promis­ing can­di­dates, and par­tic­i­pa­to­ry anno­ta­tion, advanc­ing the dis­cov­ery and char­ac­ter­i­za­tion of plant nat­ur­al prod­ucts. 

Why now?

• Data abun­dance: rapid growth of paired plant transcriptomics–metabolomics datasets unlocks path­way infer­ence at scale.
• Frag­ment­ed knowl­edge: path­way, chem­istry, and genomics data live in silos, slow­ing pre­dic­tion, val­i­da­tion, and AI-dri­ven dis­cov­ery.
• Linked open data momen­tum: com­mu­ni­ty stan­dards (Wikidata/WikiPathways) and SPAR­QL-queryable graphs make reusable, inter­op­er­a­ble sci­ence prac­ti­cal.

Fig­ure from F.C. Wolters, E. Del Pup, et al. Pair­ing omics to decode the diver­si­ty of plant spe­cial­ized metab­o­lism, Cur­rent Opin­ion in Plant Biol­o­gy 82 (2024) 102657. https://doi.org/10.1016/j.pbi.2024.102657

What we built

To achieve this vision, we devel­oped sev­er­al build­ing blocks of the knowl­edge base: 

• Updat­ed key repos­i­to­ries of plant biosyn­the­sis;
• Col­lab­o­rat­ed on a pipeline to process and anno­tate paired mul­ti-omics data in plants.

Cat­alyz­ing a com­mu­ni­ty

Dur­ing the FAIR Data Fund project, we gath­ered a com­mu­ni­ty of researchers and host­ed the sym­po­sium “Knowl­edge Graphs for Plant and Micro­bio­me Mul­ti­omics” (14th Octo­ber 2025) in Wagenin­gen. With near­ly 130 reg­is­tered par­tic­i­pants, the sym­po­sium brought togeth­er users, data gen­er­a­tors, and tool devel­op­ers in nat­ur­al prod­uct dis­cov­ery, all shar­ing the vision of build­ing a linked knowl­edge base for nat­ur­al prod­uct biosyn­the­sis. The goal of the sym­po­sium was to bring togeth­er inter­na­tion­al speak­ers work­ing at the inter­face of plant biol­o­gy, com­pu­ta­tion­al metabolomics, and seman­tic data mod­el­ing and inte­gra­tion. The cen­tral ques­tion of the day was “How can we use linked open data and knowl­edge graphs to gen­er­ate hypothe­ses in nat­ur­al prod­uct biosyn­the­sis?”. The record­ing of the sym­po­sium is avail­able on YouTube.

Tar­get­ed roadmap ses­sion

After the sym­po­sium, we host­ed a tar­get­ed dis­cus­sion “Pow­er­ing a Uni­fied Knowl­edge Base for Plant Nat­ur­al Prod­uct Dis­cov­ery” to estab­lish col­lab­o­ra­tions and find syn­er­gies between dif­fer­ent research groups and tool devel­op­ers and shape the design of the path­way knowl­edge base. By align­ing our work with the nat­ur­al prod­uct research com­mu­ni­ty, we will ensure good project gov­er­nance and sus­tain­abil­i­ty.

Open com­mu­ni­ty hub 

The tar­get­ed brain­storm­ing result­ed in a research com­mu­ni­ty that col­lects all of the indi­vid­ual efforts and projects con­nect­ed to the col­lab­o­ra­tive vision, which is now pub­licly host­ed on GitHub as a Path­way Linked Open Data Com­mu­ni­ty.

The Sym­po­sium “Knowl­edge Graphs for Plant and Micro­bio­me Mul­ti­omics” (14th Octo­ber 2025) at Wagenin­gen Uni­ver­si­ty & Research. Check the LinkedIn wrap-up post.

Build­ing pro­to­types 

The FAIR Data Fund allowed us to hire two Bioin­for­mat­ics stu­dent assis­tants (Max Muller and Ariël Komen) at Wagenin­gen Uni­ver­si­ty work­ing on essen­tial build­ing blocks of the project.

The fund­ing from the grant also allowed us to host the sym­po­sium “Knowl­edge Graphs for Plant and Micro­bio­me Mul­ti­omics” in Wagenin­gen and the fol­low-up tar­get­ed brain­storm­ing to estab­lish the research com­mu­ni­ty work­ing towards this vision. Addi­tion­al­ly, Ele­na pitched the project at the OPEN and FAIR in Nat­ur­al and Engi­neer­ing Sci­ences (NES) in Utrecht on 22 May 2025.

Ele­na Del Pup pitch­ing her project “Cat­alyz­ing plant nat­ur­al prod­uct dis­cov­ery with a com­mu­ni­ty-dri­ven linked knowl­edge base” at the OPEN and FAIR in Nat­ur­al and Engi­neer­ing Sci­ences (NES) in Utrecht on 22 May 2025.