Published June 10, 2026
| Version bgc-v1.1
Dataset
Open
PlantMetWiki BGC crosslinks: MIBiG and plantiSMASH to RDF
Authors/Creators
- 1. Wageningen University & Research
- 2. Maastricht University
Description
RDF Turtle files linking biosynthetic gene cluster (BGC) data from MIBiG (curated) and plantiSMASH (predicted) to the PlantMetWiki / WikiPathways pathway knowledge graph, derived from PlantCyc 17.0. BGCs are typed as pmw:BiosyntheticGeneCluster and connected to pathway genes via RO:0000051 (has_part). For Arabidopsis thaliana, direct SPARQL joins are enabled through shared identifiers.org/tair.name/ IRIs. Includes VoID metadata, input gene-cluster membership JSON files, and a summary table of BGC–pathway gene crosslinks (199 unique links across 38 BGCs, 50 genes, and 109 metabolic pathways for Arabidopsis thaliana).
Notes
This dataset contains RDF representations of BGC data derived from three sources with different licenses:
1. MIBiG (curated BGCs): Creative Commons Attribution 4.0 (CC BY 4.0). Cite: Terlouw et al. 2023, doi:10.1093/nar/gkac1049.
2. plantiSMASH (predicted BGCs): Creative Commons Attribution 4.0 (CC BY 4.0). Cite: Kautsar et al. 2017, doi:10.1093/nar/gkx338.
3. PlantCyc 17.0 (pathway gene annotations used for crosslinks): OPEN DATABASE LICENSE FOR THE PLANT METABOLIC NETWORK DATABASES (PMN). The databases may be used royalty-free worldwide and may be modified and redistributed, provided that derived copies clearly identify the source database(s), include applicable copyright notices and author lists, and identify or summarize modifications. See: https://plantcyc.org/?webform=license-agreement
Files
pathway-lod/map-to-rdf-bgc-v1.1.zip
Files
(2.3 MB)
| Name | Size | Download all |
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md5:d808b7026c4124b9a5ae325111455ccb
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Additional details
Related works
- Is derived from
- Dataset: 10.5281/zenodo.19928985 (DOI)
- Is part of
- Dataset: 10.5281/zenodo.17967619 (DOI)
- Is supplement to
- https://github.com/pathway-lod/map-to-rdf (URL)
- References
- Journal article: 10.1093/nar/gkac1049 (DOI)
- Journal article: 10.1093/nar/gkx338 (DOI)
Software
- Repository URL
- https://github.com/pathway-lod/map-to-rdf