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Here is an example of the results returned from VIVO to Google Refine:

No Format

{
  "q0": {
    "result": [
      {
        "id": "http://vivo.med.cornell.edu/individual/cwid-clr9010",
        "name": "Raggio, Cathleen L.",
        "score": 0.15898549556732178,
        "match": "false",
        "type": [
          {
            "id": "http://xmlns.com/foaf/0.1/Agent",
            "name": "Agent"
          },
          {
            "id": "http://vivoweb.org/ontology/core#FacultyMember",
            "name": "core:FacultyMember"
          },
          {
            "id": "http://xmlns.com/foaf/0.1/Person",
            "name": "Person"
          }
        ]
      },
      {
        "id": "http://vivo.med.cornell.edu/individual/cwid-cacres",
        "name": "Acres, Cathleen",
        "score": 0.15898549556732178,
        "match": "false",
        "type": [
          {
            "id": "http://xmlns.com/foaf/0.1/Agent",
            "name": "Agent"
          },
          {
            "id": "http://vivoweb.org/ontology/core#NonFacultyAcademic",
            "name": "core:NonFacultyAcademic"
          },
          {
            "id": "http://xmlns.com/foaf/0.1/Person",
            "name": "Person"
          }
        ]
      },
      {
        "id": "http://vivo.med.cornell.edu/individual/cwid-cal9048",
        "name": "London, Cathleen",
        "score": 0.15898549556732178,
        "match": "false",
        "type": [
          {
            "id": "http://xmlns.com/foaf/0.1/Agent",
            "name": "Agent"
          },
          {
            "id": "http://vivoweb.org/ontology/core#FacultyMember",
            "name": "core:FacultyMember"
          },
          {
            "id": "http://xmlns.com/foaf/0.1/Person",
            "name": "Person"
          }
        ]
      }
    ]
  }
}

...

See below an example of the response in json format:

No Format

jsonp1313077460641 (
  {
    "properties":
    [
      {
        "id":"http://vivoweb.org/ontology/core#faxNumber",
        "schema":{"id":"http://xmlns.com/foaf/0.1/Agent","alias":[],"name":"Agent"},
        "alias":[],"name":"fax",
        "expects":{"id":"http://vivoweb.org/ontology/core#faxNumber","alias":[],"name":"fax"}
      },
      {
        "id":"http://vivoweb.org/ontology/core#overview",
        "schema":{"id":"http://xmlns.com/foaf/0.1/Agent","alias":[],"name":"Agent"},
        "alias":[],"name":"overview",
        "expects":{"id":"http://vivoweb.org/ontology/core#overview","alias":[],"name":"overview"}
      }
    ]
  }
)

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See below an example of a query and a response:

No Format

{"query":
  [
    {
      "id":null,
      "id|=":["http://vivo.med.cornell.edu/individual/n3704","http://vivo.med.cornell.edu/individual/n3526"],
      "http://xmlns.com/foaf/0.1/firstName":  [{"optional":true,"limit":10,"name":null,"id":null,"type":[]}]
    }
  ]
}

{"result":
  [
    {"id":"http://vivo.med.cornell.edu/individual/n3704","http://xmlns.com/foaf/0.1/firstName":["Geoffrey"]},
    {"id":"http://vivo.med.cornell.edu/individual/n3526","http://xmlns.com/foaf/0.1/firstName":["Dina"]}
  ]
}

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  1. Make sure the following are installed on the desired machine:
  2. :Java (SE) 1.6 or higher, http://java.sun.com
  3. :Apache Ant 1.7 or higher, http://ant.apache.org
  4. Download Google Refine version 2.5 from httphttps://code.googlegithub.com/p/google-refine/OpenRefine/OpenRefine/wiki/Downloads. If you have Subversion installed and access to a command line, you can use the following command to checkout the 2.5 release:
  5. :svn checkout http://google-refine.googlecode.com/svn/tags/2.5 grefine-googlecode-2.5
  6. Download the VIVO plugin and Google Refine extension from http://sourceforge.net/projects/vivo/files/Utilities, or click on one of the following links:
    :grefine-vivo-1.5.tar.gz or grefine-vivo-1.5.zip
  7. :Unpack and you will find the following files and folder: i) grefine-vivo-extension; ii) README
  8. Download and install VIVO release version 1.5 from http://sourceforge.net/projects/vivo/files/, if you have not already done so.

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  1. Copy grefine-vivo-extension to Google Refine's extension folder so that it becomes /extension/grefine-vivo-extension
  2. Rename from /extension/grefine-vivo-extension to /extension/vivo (required)
  3. Modify /extensions/build.xml to add vivo to build and clean:

    Panel

    <target name="build">
    <echo message="Building extensions" />
    <ant dir="sample/" target="build" />
    <ant dir="jython/" target="build" />
    <ant dir="freebase/" target="build" />
    <ant dir="gdata/" target="build" />
    <ant dir="vivo/" target="build" />
    </target>
    <target name="clean">
    <echo message="cleaning extensions" />
    <ant dir="sample/" target="clean" />
    <ant dir="jython/" target="clean" />
    <ant dir="freebase/" target="clean" />
    <ant dir="gdata/" target="clean" />
    <ant dir="vivo/" target="clean" />
    </target>

  4. Run ./refine clean
  5. Run ./refine build
  6. To start Google Refine, run ./refine

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