{
  "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/2006/04/04/mining-kegg-pathway-database-with-self.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/tzwfe-ww931",
      "url": "https://chem-bla-ics.linkedchemistry.info/2006/04/04/mining-kegg-pathway-database-with-self.html",
      "title": "Mining the KEGG pathway database with self-organizing maps",
      "content_html": "<p>The <a href=\"https://en.wikipedia.org/wiki/Self_organizing_map\">Self-organizing map</a> (SOM) is a popular (again) and intuitive non-linear mapping\nmethod: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and\n<a href=\"http://www.dq.fct.unl.pt/staff/jas/\">Aires-de-Sousa</a> published a paper that uses this method to analyze the whole\n<a href=\"http://www.genome.jp/kegg/pathway.html\">KEGG pathway database</a>: <em>Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics\nApproach</em> (DOI: <a href=\"https://doi.org/10.1002/anie.200503833\">anie.200503833</a>).</p>\n\n<p>The method is based on earlier work by Zhang and Aires-de-Sousa: <em>Structure-Based Classification of Chemical Reactions without Assignment\nof Reaction Centers</em> (DOI: <a href=\"https://doi.org/10.1021/ci0502707\">10.1021/ci0502707</a>). A non-trivial feature of the suggested method is the\nuse of two SOMs. The first maps the reaction onto a fixed-length vector (coined MOLMAP), which is used as input vector for the second map.\nThis later map is used to cluster the KEGG reactions on a purely chemical basis. The resemblence with the\n<a href=\"https://en.wikipedia.org/wiki/EC_number\">EC numbering system</a> is striking.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Latino, D. A. R. S., &#38; Aires‐de‐Sousa, J. (2006). Genome‐Scale Classification of Metabolic Reactions: A Chemoinformatics Approach. <i>Angewandte Chemie International Edition</i>, <i>45</i>(13), 2066–2069. https://doi.org/10.1002/anie.200503833 <a href=\"https://doi.org/10.1002/ANIE.200503833\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1002/ANIE.200503833\">Scholia</a></div>\n    <div class=\"csl-entry\">Zhang, Q.-Y., &#38; Aires-de-Sousa, J. (2005). Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers. <i>Journal of Chemical Information and Modeling</i>, <i>45</i>(6), 1775–1783. https://doi.org/10.1021/ci0502707 <a href=\"https://doi.org/10.1021/CI0502707\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1021/CI0502707\">Scholia</a></div>\n  </div>",
      "summary": "The Self-organizing map (SOM) is a popular (again) and intuitive non-linear mapping method: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and Aires-de-Sousa published a paper that uses this method to analyze the whole KEGG pathway database: Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach (DOI: anie.200503833).",
      
      "date_published": "2006-04-04T00:00:00+00:00",
      "date_modified": "2025-02-16T00:00:00+00:00",
      "tags": ["kegg","chemometrics"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1002/ANIE.200503833", "doi": "10.1002/ANIE.200503833"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.1021/CI0502707", "doi": "10.1021/CI0502707"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}