SPARQLing Plant Metabolic Pathways Wiki

Documentation and Tutorial for the PlantMetWiki SPARQL Explorer

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Summary

Plant Metabolic Pathways Wiki (PlantMetWiki) is an open online portal for querying linked specialized plant pathway information. PlantMetWiki is available in Semantic Web format as Resource Description Framework (RDF) and can be accessed via an easy-to-use SNORQL user interface. Pre-written SPARQL queries are available for users to execute or adapt to retrieve pathway information. Federated queries with other linked open data tools are supported, thereby expanding the Wikidata framework.

By structuring characterized pathways knowledge as Linked Open Data, linking it to predicted biosynthetic clusters, and supporting federated querying, PlantMetWiki supports hypothesis generation in plant biosynthesis and natural product discovery.

Using the SPARQL Explorer

Visit our PlantMetWiki SPARQL interface at plantmetwiki.bioinformatics.nl.

Follow the steps below to execute a pre-written query:

1: Select a query from the list of example SPARQL queries. You can adapt the query by typing in the SPARQL Query box or from the source repository pathway-lod/SPARQLQueries

2: Press the green Query button to execute your selected query.

3: View the result s on the same page.

4: You can select your own list of example queries from github, by adding the link and click the refresh button.

New Snorql Interface

Download Results

Output data is available for download in native RDF format (.ttl), TSV, CSV, and json.

Use Cases

PlatMetWiki supports generating insights and hypotheses from plant metabolism to other research areas, including biomarker discovery, toxicology, precision nutrition, and forensic (wildlife) sciences.

Some examples include:

1. Resolving pathways across species: an example in Capsicum

Focus: Multispecies pathway modeling and cross-species inference

Incomplete pathway annotations are common in plant metabolism. This tutorial shows how PlantMetWiki can be used to compare pathway information across related species and leverage shared reactions, substrates, and products to resolve missing biosynthetic steps.

Research question:
If a reaction or enzyme is present in Capsicum annuum but missing in Capsicum frutescens, can its presence be inferred based on shared pathway context across species?

👉 Read the full tutorial →

2. Diving into natural products: an example from castor oil

Focus: Molecule-centric exploration of biosynthesis and chemistry

Natural product research often starts from a molecule rather than a pathway. This tutorial demonstrates how PlantMetWiki can be used to identify the plant pathways and species associated with specific natural product molecules, and how this information can be enriched with external chemical knowledge using federated queries.

Research question:
Which plant species and biosynthetic pathways are associated with natural product molecules found in castor oil, and how can their biochemical context be explored using linked open data?

👉 Read the full tutorial on Castor oil →

👉 Read the full tutorial on Theobromine →

Tutorial Pages : the SPARQL PlantMetWiki Explorer

Resources

PlantMetWiki architecture

PlantMetWiki is built as a modular Linked Open Data ecosystem. The following repositories together form the data pipeline, infrastructure, user interfaces, and documentation of the project:

Data availability

Data related to PlantMetWiki is available at Zenodo PlantMetWiki Community.