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.
- Update your SPARQL query from this template
Download Results
Output data is available for download in native RDF format (.ttl), TSV, CSV, and json.
Use Cases
1. Diving into Natural Products : and example from castor oil
2. Resolving Pathways across Species : an example in Capsicum
Tutorial Pages : the SPARQL PlantMetWiki Explorer
Resources
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Introduction to RDF and SPARQL by BiGCaT Maastricht University
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Wikipathway ontology The WikiPathways WP Ontology
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:
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Cyc_to_wiki – Data extraction and preparation from pathway databases
https://github.com/pathway-lod/Cyc_to_wiki -
gpml-to-rdf – Conversion of GPML pathway files into RDF
https://github.com/pathway-lod/gpml-to-rdf -
map-to-rdf – Generation of RDF crosslinks with MIBiG and plantiSMASH
https://github.com/pathway-lod/map-to-rdf -
virtuoso-httpd-docker – Triple store setup and Dockerized deployment of the PlantMetWiki SPARQL endpoint
https://github.com/pathway-lod/virtuoso-httpd-docker -
Snorql-UI – Web-based SPARQL query interface for PlantMetWiki
https://github.com/pathway-lod/Snorql-UI -
SPARQLQueries – Curated example SPARQL queries for PlantMetWiki and federated endpoints
https://github.com/pathway-lod/SPARQLQueries -
SPARQLTutorials – Documentation and tutorial pages for learning how to query PlantMetWiki (this website)
https://github.com/pathway-lod/SPARQLTutorials
Data availability
Data related to PlantMetWiki is available at Zenodo PlantMetWiki Community.