Dataset Open Access

Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup


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{
  "description": "<ul>\n\t<li>Eight versions of COBRA-compliant SBML files are available for each Recon 2M.1 and Recon 2M.2 depending on the use of: MNXref versus BiGG IDs; Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).</li>\n\t<li>892 personal GEMs (only T-GEMs) built with Recon 2.2</li>\n\t<li>1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1</li>\n\t<li>892 personal GEMs (only T-GEMs) built with Recon 2M.2</li>\n</ul>\n\n<p>\u00a0</p>\n\n<p><strong>Publication</strong></p>\n\n<p>Jae Yong Ryu<sup>1</sup>, Hyun Uk Kim<sup>1</sup> &amp; Sang Yup Lee<sup>*</sup>. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., <em>Proc. Natl. Acad. Sci. U.S.A.</em>, 2017, http://www.pnas.org/content/early/2017/10/23/1713050114</p>\n\n<p>\u00a0</p>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea", 
      "@type": "Person", 
      "name": "Ryu, Jae Yong"
    }, 
    {
      "affiliation": "Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea", 
      "@type": "Person", 
      "name": "Kim, Hyun Uk"
    }, 
    {
      "affiliation": "Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea", 
      "@type": "Person", 
      "name": "Lee, Sang Yup"
    }
  ], 
  "url": "https://zenodo.org/record/583326", 
  "datePublished": "2017-05-28", 
  "keywords": [
    "Human genome-scale metabolic model", 
    "Recon", 
    "Gene-transcript-protein-reaction associations (GeTPRA)", 
    "Protein isoform"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Personal_TCGA_GEMs_using_recon2.2.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Personal_TCGA_GEMs_using_recon2M.1.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Personal_TCGA_GEMs_using_recon2M.2.zip", 
      "@type": "DataDownload", 
      "fileFormat": "zip"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_BiGG_Ensembl_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_BiGG_Entrez_Gene.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_BiGG_RefSeq_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_BiGG_UCSC_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_MNX_Ensembl_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_MNX_Entrez_Gene.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_MNX_RefSeq_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.1_MNX_UCSC_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_BiGG_Ensembl_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_BiGG_Entrez_Gene.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_BiGG_RefSeq_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_BiGG_UCSC_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_MNX_Ensembl_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_MNX_Entrez_Gene.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_MNX_RefSeq_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/3260f250-f903-417d-b772-d16e205e8616/Recon2M.2_MNX_UCSC_Transcript.xml", 
      "@type": "DataDownload", 
      "fileFormat": "xml"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.583326", 
  "@id": "https://doi.org/10.5281/zenodo.583326", 
  "@type": "Dataset", 
  "name": "Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism"
}
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