{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2026/01/05/plantmetwiki.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/wyz5v-vts33", "url": "https://chem-bla-ics.linkedchemistry.info/2026/01/05/plantmetwiki.html", "title": "PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge", "content_html": "

Back on October I presented Everything you always wanted to know: plant pathway modelling in WikiPathways (doi:10.5281/zenodo.18149988)\nat the Knowledge Graphs for Plant and Microbiome Multiomics symposium (see this archived LinkedIn post)\non 14th October 2025 (youtube recording).\nI had not found time yet to post about this meeting, but it was an awesome list of speakers, regrettable absense of some others, but resulting\nin new contacts and some slowly evolving collaborations.

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Previously, plant pathways were somewhat negatively prioritized at our BiGCaT research group. Something with Dutch academic politics. But that\nwas 10 years ago, and with the notion that human health very much involves the exposome, which includes live around humans, I think the\nplant pathway science is important to human health. Even just the human health impacts of drops in biodiversity. Or the impact on our\nnutrition supply chain of climate change.

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Anyway, I am happy that Elena and Denise\npulled me into a collaboration to create an RDF-based knowledge graph about plant pathways.\nTheir idea was to PlantCyc pathways (their license seems to allow that; doi:10.1093/nar/gkae991),\nconvert that to GPML (by Max) and then to RDF. That last step is where I come in. The details will follow later, but Elena announced\nthe project on LinkedIn (archived link),\nso time to blog about it myself too.

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I am happy with this effort, not just because we now have pathways in RDF form for more than 500 species, but also\nbecause it requires continued development of the WikiPathways solutions, like GPML and\nlibGPML and the RDF generation\ncode, but also BridgeDb (doi:10.1186/1471-2105-11-5).\nThe latter provides the identifier mapping infrastructure, but needed to be extended for\nthe new species (something I had to do earlier this year for several caffeine synthesis pathways\ndeveloped at the DBCLS BioHackathon 2025).

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Lars gave me a tip on how to scale this up (after a manual addition),\nverifier.globalnames.org (doi:10.5281/zenodo.17245658,\nwhich greatly helped me out. It translates species names\ninto identifiers, and their JSON is very rich in that process as well as easy to process. So,\na custom script allowed me to update BridgeDb more efficiently. Highly recommended!

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So, the resulting knowledge base is available at plantmetwiki.bioinformatics.nl\nand looks like this (also big thanks to Marvin for support in setting this up!):

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References

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Hawkins, C., Xue, B., Yasmin, F., Wyatt, G., Zerbe, P., & Rhee, S. Y. (2024). Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data. Nucleic Acids Research, 53(D1), D1606–D1613. https://doi.org/10.1093/nar/gkae991 CrossRef Scholia
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Mozzherin, D. (2025). GNverifier -- a reconciler and resolver of scientific names against more than 100 data sources. (Version v1.3.0) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.17245658 CrossRef Scholia
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van Iersel, M. P., Pico, A. R., Kelder, T., Gao, J., Ho, I., Hanspers, K., Conklin, B. R., & Evelo, C. T. (2010). The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-5 CrossRef Scholia
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Willighagen, E. (2025). Everything you always wanted to know: plant pathway modelling in WikiPathways. Zenodo. https://doi.org/10.5281/ZENODO.18149988 CrossRef Scholia
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", "summary": "Back on October I presented Everything you always wanted to know: plant pathway modelling in WikiPathways (doi:10.5281/zenodo.18149988) at the Knowledge Graphs for Plant and Microbiome Multiomics symposium (see this archived LinkedIn post) on 14th October 2025 (youtube recording). I had not found time yet to post about this meeting, but it was an awesome list of speakers, regrettable absense of some others, but resulting in new contacts and some slowly evolving collaborations.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/plantmetwiki.png", "date_published": "2026-01-05T00:00:00+00:00", "date_modified": "2026-01-05T00:00:00+00:00", "tags": ["wikipathways","gpml","rdf"], "_references": [ { "url": "https://doi.org/10.5281/zenodo.18149988", "doi": "10.5281/zenodo.18149988" } , { "url": "https://doi.org/10.1093/nar/gkae991", "doi": "10.1093/nar/gkae991" } , { "url": "https://doi.org/10.1186/1471-2105-11-5", "doi": "10.1186/1471-2105-11-5" } , { "url": "https://doi.org/10.5281/zenodo.17245658", "doi": "10.5281/zenodo.17245658" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }