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PlantMetWiki BGC crosslinks: MIBiG and plantiSMASH to RDF

Authors: Del Pup, Elena; Slenter, Denise;

PlantMetWiki BGC crosslinks: MIBiG and plantiSMASH to RDF

Abstract

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

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).

Related Organizations
Keywords

WikiPathways, Arabidopsis thaliana, VoID, linked data, SPARQL, biosynthetic gene clusters, RDF, plant metabolism, PlantMetWiki, plantiSMASH, PlantCyc, MIBiG

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average