New paper: "WikiPathways 2024: next generation pathway database"
This week the next WikiPathways NAR Database issue paper was published (doi:10.1093/nar/gkad960). It is the next paper in a series of papers about the evolution of the Open Science project for making biological pathways available in a Open and FAIR way. This year, it described that significant move away from MediaWiki. It simply was too costly to keep up with the upstream code base (think: more than 200 thousand euro costly). This paper describes a transition to a modular system with Jekyll and Markdown as new platform technologies. The full details are available as open notebook science: everything is basically a git repository.
The is the workflow of what the new platform does when a new pathway (version) gets added to WikiPathways:
The upgrade of the whole stack is, however, in full swing. Not everything has migrated yet and the RDF generation is not for example.
Additional details
Description
This week the next WikiPathways NAR Database issue paper was published (doi:10.1093/nar/gkad960). It is the next paper in a series of papers about the evolution of the Open Science project for making biological pathways available in a Open and FAIR way. This year, it described that significant move away from MediaWiki.
Identifiers
- GUID
- https://doi.org/10.59350/8pkga-q4n03
- URL
- https://chem-bla-ics.linkedchemistry.info/2023/11/11/wikipathways-nar.html
Dates
- Issued
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2023-11-11T01:00:00
- Updated
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2023-11-11T01:00:00
References
- Agrawal, A., Balcı, H., Hanspers, K., Coort, S. L., Martens, M., Slenter, D. N., Ehrhart, F., Digles, D., Waagmeester, A., Wassink, I., Abbassi-Daloii, T., Lopes, E. N., Iyer, A., Acosta, J. M., Willighagen, L. G., Nishida, K., Riutta, A., Basaric, H., Evelo, C. T., … Pico, A. R. (2023). WikiPathways 2024: next generation pathway database. Nucleic Acids Research, 52(D1), D679–D689. https://doi.org/10.1093/nar/gkad960