OpenRefine Script to Extract Authors and EntrezUIDs from a PubMed CSV file

author_extract

[
  {
    "op": "core/column-removal",
    "description": "Remove column URL",
    "columnName": "URL"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Details",
    "columnName": "Details"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column ShortDetails",
    "columnName": "ShortDetails"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Resource",
    "columnName": "Resource"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Type",
    "columnName": "Type"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Identifiers",
    "columnName": "Identifiers"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Db",
    "columnName": "Db"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Properties",
    "columnName": "Properties"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Column 12",
    "columnName": "Column 12"
  },
  {
    "op": "core/row-removal",
    "description": "Remove rows",
    "engineConfig": {
      "facets": [
        {
          "query": "Descri",
          "name": "Description",
          "caseSensitive": false,
          "columnName": "Description",
          "type": "text",
          "mode": "text"
        }
      ],
      "mode": "row-based"
    }
  },
  {
    "op": "core/multivalued-cell-split",
    "description": "Split multi-valued cells in column Description",
    "columnName": "Description",
    "keyColumnName": "Description",
    "separator": ",",
    "mode": "plain"
  },
  {
    "op": "core/multivalued-cell-split",
    "description": "Split multi-valued cells in column Description",
    "columnName": "Description",
    "keyColumnName": "Description",
    "separator": ";",
    "mode": "plain"
  },
  {
    "op": "core/fill-down",
    "description": "Fill down cells in column EntrezUID",
    "engineConfig": {
      "facets": [],
      "mode": "row-based"
    },
    "columnName": "EntrezUID"
  },
  {
    "op": "core/mass-edit",
    "description": "Mass edit cells in column Description",
    "engineConfig": {
      "facets": [
        {
          "query": "marmot",
          "name": "Description",
          "caseSensitive": false,
          "columnName": "Description",
          "type": "text",
          "mode": "text"
        }
      ],
      "mode": "row-based"
    },
    "columnName": "Description",
    "expression": "value",
    "edits": [
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Marmot MG",
          "Marmot MG."
        ],
        "to": "Marmot MG"
      },
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Marmot M",
          "Marmot M."
        ],
        "to": "Marmot MG"
      }
    ]
  },
  {
    "op": "core/mass-edit",
    "description": "Mass edit cells in column Description",
    "engineConfig": {
      "facets": [],
      "mode": "row-based"
    },
    "columnName": "Description",
    "expression": "value",
    "edits": [
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Kivimaki M",
          "Kivimäki M",
          "Kivimäki M.",
          "Kivimaki M."
        ],
        "to": "Kivimaki M"
      },
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Ferrie JE",
          "Ferrie JE."
        ],
        "to": "Ferrie JE"
      },
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Lawlor DA",
          "Lawlor DA."
        ],
        "to": "Lawlor DA"
      },
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Bobak M.",
          "Bobak M"
        ],
        "to": "Bobak M"
      },
      {
        "fromBlank": false,
        "fromError": false,
        "from": [
          "Adamkova V",
          "Adamková V"
        ],
        "to": "Adamková V"
      }
    ]
  },
  {
    "op": "core/row-removal",
    "description": "Remove rows",
    "engineConfig": {
      "facets": [
        {
          "query": "et al",
          "name": "Description",
          "caseSensitive": false,
          "columnName": "Description",
          "type": "text",
          "mode": "text"
        }
      ],
      "mode": "row-based"
    }
  },
  {
    "op": "core/text-transform",
    "description": "Text transform on cells in column Description using expression grel:value.substring(0,-1)",
    "engineConfig": {
      "facets": [
        {
          "query": ".",
          "name": "Description",
          "caseSensitive": false,
          "columnName": "Description",
          "type": "text",
          "mode": "text"
        }
      ],
      "mode": "row-based"
    },
    "columnName": "Description",
    "expression": "grel:value.substring(0,-1)",
    "onError": "keep-original",
    "repeat": false,
    "repeatCount": 10
  },
  {
    "op": "core/column-rename",
    "description": "Rename column Description to CoAuthors",
    "oldColumnName": "Description",
    "newColumnName": "CoAuthors"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column Title",
    "columnName": "Title"
  }
]