{
  "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/2007/08/13/centralized-or-decentralized.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/y11ff-5he48",
      "url": "https://chem-bla-ics.linkedchemistry.info/2007/08/13/centralized-or-decentralized.html",
      "title": "Centralized or decentralized?",
      "content_html": "<p><a href=\"http://wwmm.ch.cam.ac.uk/blogs/murrayrust/\">Peter</a> wondered if data should be stored <a href=\"http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=497\">centralized or decentralized</a>,\nwhen <a href=\"http://mndoci.com/blog/\">Deepak</a> <a href=\"http://mndoci.com/blog/2007/08/12/freebase-at-scifoo/\">blogged</a> about\n<a href=\"http://freebase.com/\">Freebase</a> and <a href=\"http://www.metaweb.com/\">Metaweb</a>. Now, I haven’t really looked into these\ntwo projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world\nwide web; it’s the PubChem compound ID versus the InChI; it’s <a href=\"http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4\">http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4</a>\nversus <code class=\"language-plaintext highlighter-rouge\">info:inchi/InChI=1/CH4/h1H4</code> (see <a href=\"https://chem-bla-ics.linkedchemistry.info/2007/07/31/rdf-ing-molecular-space.html\">RDF-ing molecular space <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).</p>\n\n<p>Both have advantages and disadvantages (everything does). Google has a huge experience with massive data, and\nis the centralized version of the distributed world wide web. Personally, I tend towards the decentralized\nversion of things. Scales better. The chemical RDF community showed some concerns about scalability of triple\nstores (see e.g. Taylor et al. <em>Bringing Chemical Data onto the Semantic Web</em>, <strong>2006</strong>, DOI <a href=\"https://doi.org/10.1021/ci050378m\">10.1021/ci050378m</a>).\nNow, their tests went up to some 30M triples, which is barely enough to store the InChI, PubChem compound ID, and one chemical name.</p>\n\n<p>So, how would this work for molecules then? I am leaning towards a system where one can query resources about\none molecule, and work ones way through molecular space. Using KEGG, reaction databases, similarity stores,\none could move from molecule to molecule, and add bits of RDF along the way, filling a local RDF store around\nthe actual query I have in mind. For example, if I want to verify that the mass spectrum I found really belongs\nto the molecular structure I have in mind, I would look up in the resources I know about all triples that\nrelate to the putative structure, and do my queries from there. That’s what I would do… (and will do, but\nmore on that later…)</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Taylor, K. R., Gledhill, R. J., Essex, J. W., Frey, J. G., Harris, S. W., &#38; De Roure, D. C. (2006). Bringing Chemical Data onto the Semantic Web. <i>Journal of Chemical Information and Modeling</i>, <i>46</i>(3), 939–952. https://doi.org/10.1021/ci050378m <a href=\"https://doi.org/10.1021/ci050378m\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1021/ci050378m\">Scholia</a></div>\n  </div>",
      "summary": "Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven’t really looked into these two projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world wide web; it’s the PubChem compound ID versus the InChI; it’s http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4 versus info:inchi/InChI=1/CH4/h1H4 (see RDF-ing molecular space ).",
      
      "date_published": "2007-08-13T00:00:00+00:00",
      "date_modified": "2025-02-16T00:00:00+00:00",
      "tags": ["inchi","semweb"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1021/ci050378m", "doi": "10.1021/ci050378m"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}