{
  "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/2012/03/04/chembl-13-as-rdf.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/qtjby-n6m67",
      "url": "https://chem-bla-ics.linkedchemistry.info/2012/03/04/chembl-13-as-rdf.html",
      "title": "ChEMBL 13 as RDF",
      "content_html": "<p><strong>Update</strong>: this work is now described in <a href=\"https://chem-bla-ics.linkedchemistry.info/2013/05/09/new-paper-chembl-database-as-linked.html\">this paper <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.</p>\n\n<p>Last week, ChEMBL 13 was <a href=\"http://chembl.blogspot.com/2012/02/chembl-13-released.html\">released</a>, with even more data, data fixes,\n<a href=\"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_13/chembl_13_release_notes.txt\">etc</a>. Since my RDF for\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2011/04/21/chembl-09-as-rdf.html\">ChEMBL 09 <i class=\"fa-solid fa-recycle fa-xs\"></i></a> my workflow has become\n<a href=\"https://github.com/egonw/chembl.rdf/commits/master\">more solid</a> and uses more common ontologies, started using more common ontologies\nand ontologies I just like, such as <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025513\">CHEMINF</a> and\n<a href=\"http://www.jbiomedsem.com/content/1/S1/S6\">CiTO</a>. Below is an overview of the resource types present in the RDF:\nactivities (almost 7M now), chemical entities, assays, targets, and documents.</p>\n\n<p><img src=\"/assets/images/relations.png\" alt=\"\" /></p>\n\n<p>The <a href=\"https://chem-bla-ics.linkedchemistry.info/2011/10/22/chembl-rdf-uploading-data-to-kasabi.html\">data on Kasabi <i class=\"fa-solid fa-recycle fa-xs\"></i></a> will be updated soon,\nand the <a href=\"http://rdf.farmbio.uu.se/chembl/sparql\">SPARQL end point</a> hosted by Uppsala University was updated yesterday, including the\n<a href=\"http://rdf.farmbio.uu.se/chembl/snorql/\">SNORQL frontend</a>:</p>\n\n<p><img src=\"/assets/images/chemblRDF13.png\" alt=\"\" /></p>\n\n<p>The new data is not fully backwards compatible. The changes to the RDF include the use of <code class=\"language-plaintext highlighter-rouge\">cito:citesAsDataSource</code>, more typing\nusing existing ontologies, e.g. with <code class=\"language-plaintext highlighter-rouge\">cheminf:CHEMINF_000000</code> and <code class=\"language-plaintext highlighter-rouge\">pro:PR_000000001</code> from the\n<a href=\"http://pir.georgetown.edu/pro/\">PRotein Ontology</a>.</p>\n\n<p>A paper dedicated to the ChEMBL-RDF is in preparation. Existing use cases can be found\n<a href=\"http://www.jbiomedsem.com/content/2/S1/S6\">here</a>.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Hastings, J., Chepelev, L., Willighagen, E., Adams, N., Steinbeck, C., &#38; Dumontier, M. (2011). The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web. <i>PLoS ONE</i>, <i>6</i>(10), e25513. https://doi.org/10.1371/journal.pone.0025513 <a href=\"https://doi.org/10.1371/JOURNAL.PONE.0025513\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1371/JOURNAL.PONE.0025513\">Scholia</a></div>\n    <div class=\"csl-entry\">Shotton, D. (2010). CiTO, the Citation Typing Ontology. <i>Journal of Biomedical Semantics</i>, <i>1</i>(S1). https://doi.org/10.1186/2041-1480-1-s1-s6 <a href=\"https://doi.org/10.1186/2041-1480-1-S1-S6\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/2041-1480-1-S1-S6\">Scholia</a></div>\n    <div class=\"csl-entry\">Willighagen, E. L., Alvarsson, J., Andersson, A., Eklund, M., Lampa, S., Lapins, M., Spjuth, O., &#38; Wikberg, J. E. (2011). Linking the Resource Description Framework to cheminformatics and proteochemometrics. <i>Journal of Biomedical Semantics</i>, <i>2</i>(S1). https://doi.org/10.1186/2041-1480-2-s1-s6 <a href=\"https://doi.org/10.1186/2041-1480-2-S1-S6\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/2041-1480-2-S1-S6\">Scholia</a></div>\n  </div>",
      "summary": "Update: this work is now described in this paper .",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/relations.png",
      "date_published": "2012-03-04T00:00:00+00:00",
      "date_modified": "2024-11-02T00:00:00+00:00",
      "tags": ["chembl","rdf","semweb","ontology","cheminf","cito"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1371/JOURNAL.PONE.0025513", "doi": "10.1371/JOURNAL.PONE.0025513"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.1186/2041-1480-1-S1-S6", "doi": "10.1186/2041-1480-1-S1-S6"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.1186/2041-1480-2-S1-S6", "doi": "10.1186/2041-1480-2-S1-S6"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}