{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      },
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/crate/1.1"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
        }
      ]
    },
    {
      "@id": "ro-crate-preview.html",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      }
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "mainEntity": {
        "@id": "humanmine.ipynb"
      },
      "datePublished": "2022-07-12 11:04:36 +0100",
      "author": [
        {
          "@id": "https://orcid.org/0000-0002-1789-1861"
        }
      ],
      "license": "BSD-2-Clause",
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.242.1",
      "url": "https://workflowhub.eu/workflows/242/ro_crate?version=1",
      "name": "Research Object Crate for Diabetes related genes expressed in pancreas",
      "description": "# Summary\nThis notebook shows how to integrate genomic and image data resources. This notebook looks at the question **Which diabetes related genes are expressed in the pancreas?** \n\nSteps:\n\n* Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.\n* Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.\n* \nWe use the [intermine Python API](https://github.com/intermine/intermine-ws-python) and the IDR Python API.\n\nThe notebook can be opened in [Colab](https://colab.research.google.com/github/IDR/idr-notebooks/blob/master/humanmine.ipynb)\n\n# Inputs\nParameters needed to configure the workflow:\n\n* TISSUE = \"Pancreas\" \n* DISEASE = \"diabetes\"\n\n# Ouputs\n* List of genes found using [HumanMine](https://pubmed.ncbi.nlm.nih.gov/35820040/)\n* List of images from IDR for one of the gene found",
      "isBasedOn": "https://github.com/IDR/idr-notebooks",
      "sdDatePublished": "2026-04-21 12:27:59 +0100",
      "creativeWorkStatus": "Stable",
      "hasPart": [
        {
          "@id": "humanmine.ipynb"
        },
        {
          "@id": "HumanMineIDR.png"
        }
      ]
    },
    {
      "@id": "humanmine.ipynb",
      "@type": [
        "File",
        "SoftwareSourceCode",
        "ComputationalWorkflow"
      ],
      "url": "https://github.com/IDR/idr-notebooks/blob/master/humanmine.ipynb",
      "contentSize": 0,
      "programmingLanguage": {
        "@id": "#jupyter"
      },
      "image": {
        "@id": "HumanMineIDR.png"
      },
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/"
      },
      "description": "# Summary\nThis notebook shows how to integrate genomic and image data resources. This notebook looks at the question **Which diabetes related genes are expressed in the pancreas?** \n\nSteps:\n\n* Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.\n* Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.\n* \nWe use the [intermine Python API](https://github.com/intermine/intermine-ws-python) and the IDR Python API.\n\nThe notebook can be opened in [Colab](https://colab.research.google.com/github/IDR/idr-notebooks/blob/master/humanmine.ipynb)\n\n# Inputs\nParameters needed to configure the workflow:\n\n* TISSUE = \"Pancreas\" \n* DISEASE = \"diabetes\"\n\n# Ouputs\n* List of genes found using [HumanMine](https://pubmed.ncbi.nlm.nih.gov/35820040/)\n* List of images from IDR for one of the gene found",
      "name": "Diabetes related genes expressed in pancreas",
      "keywords": "",
      "version": 1,
      "license": "https://spdx.org/licenses/BSD-2-Clause",
      "creator": {
        "@id": "https://workflowhub.eu/people/144"
      },
      "producer": {
        "@id": "https://workflowhub.eu/projects/69"
      },
      "dateCreated": "2021-11-23T11:28:07Z",
      "dateModified": "2026-02-19T16:17:04Z",
      "isPartOf": [
        {
          "@id": "https://workflowhub.eu/collections/4"
        },
        {
          "@id": "https://workflowhub.eu/collections/36"
        }
      ],
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.242.1",
      "input": [

      ],
      "output": [

      ],
      "sdPublisher": {
        "@id": "https://about.workflowhub.eu/"
      }
    },
    {
      "@id": "HumanMineIDR.png",
      "@type": [
        "File",
        "ImageObject"
      ],
      "contentSize": 1135634
    },
    {
      "@id": "https://orcid.org/0000-0002-1789-1861",
      "@type": "Person",
      "name": "Jean-Marie Burel",
      "identifier": "https://orcid.org/0000-0002-1789-1861"
    },
    {
      "@id": "https://workflowhub.eu/people/144",
      "@type": "Person",
      "name": "Jean-Marie Burel"
    },
    {
      "@id": "https://workflowhub.eu/projects/69",
      "@type": [
        "Project",
        "Organization"
      ],
      "name": "OME"
    },
    {
      "@id": "https://workflowhub.eu/collections/4",
      "@type": "Collection",
      "name": "IDR"
    },
    {
      "@id": "https://workflowhub.eu/collections/36",
      "@type": "Collection",
      "name": "IDR searcher"
    },
    {
      "@id": "#jupyter",
      "@type": "ComputerLanguage",
      "name": "Jupyter",
      "identifier": {
        "@id": "https://jupyter.org/"
      },
      "url": {
        "@id": "https://jupyter.org/"
      }
    },
    {
      "@id": "https://about.workflowhub.eu/",
      "@type": "Organization",
      "name": "WorkflowHub",
      "url": "https://about.workflowhub.eu/"
    }
  ]
}