{
  "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/2023/11/11/wikipathways-nar.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/10.59350/8pkga-q4n03",
      "url": "https://chem-bla-ics.linkedchemistry.info/2023/11/11/wikipathways-nar.html",
      "title": "New paper: "WikiPathways 2024: next generation pathway database"",
      "content_html": "<p>This week the next <a href=\"https://wikipathways.org/\">WikiPathways</a> <a href=\"https://academic.oup.com/nar/search-results?f_TocHeadingTitle=Database+Issue\">NAR Database</a>\nissue paper was published (doi:<a href=\"https://doi.org/10.1093/nar/gkad960\">10.1093/nar/gkad960</a>). It is the next\npaper in a series of papers about the evolution of the Open Science project for\nmaking biological pathways available in a Open and FAIR way. This year, it described\nthat significant move away from <a href=\"https://en.wikipedia.org/wiki/MediaWiki\">MediaWiki</a>.\nIt simply was too costly to keep up with the upstream code base (think: more than 200\nthousand euro costly). This paper describes a transition to a modular system with\n<a href=\"https://en.wikipedia.org/wiki/Jekyll_(software)\">Jekyll</a> and Markdown as\nnew platform technologies. The full details are available as open notebook science:\neverything is basically a git repository.</p>\n\n<p>The is the workflow of what the new platform does when a new pathway (version) gets\nadded to WikiPathways:</p>\n\n<p><img src=\"/assets/images/wp-gpml-change-workflow.png\" alt=\"Workflow that is triggered by an added or changed GPML file, eventually triggering an update of the website.\" /></p>\n\n<p>The upgrade of the whole stack is, however, in full swing. Not everything has\nmigrated yet and the RDF generation is not for example.</p>\n\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">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. <i>Nucleic Acids Research</i>, <i>52</i>(D1), D679–D689. https://doi.org/10.1093/nar/gkad960 <a href=\"https://doi.org/10.1093/NAR/GKAD960\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1093/NAR/GKAD960\">Scholia</a></div>\n  </div>",
      "summary": "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.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/wp-gpml-change-workflow.png",
      "date_published": "2023-11-11T00:00:00+00:00",
      "date_modified": "2023-11-11T00:00:00+00:00",
      "tags": ["wikipathways","git"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1093/NAR/GKAD960", "doi": "10.1093/NAR/GKAD960"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}