maDMPs

Services

There are several services defined in the database which have corresponding subfolders in this project. Each services either downloads data via an API or loads it via a file manually placed in the service's /tmp directory. The service then transforms that data into a standardized JSON format.

Berkeley Biocode

The Berkeley Biocode site currently houses the GUMP Moorea research station project metadata: http://bnhmipt.berkeley.edu/ipt/resource?r=biocode. This information will be moving to the GeOMe project. The EML file must be manually downloaded and placed into the biocode/tmp/biocode.xml directory

GeOMe

The Genomic Observatories Metadatabase (GeOMe) contains project, and dataset metadata. The service retrieves data directly from GeOMe via their public API.

This program was based on the R program referenced on the GeOMe website. The underlying code makes HTTPS calls to the FIMS API to query the GeOMe database and retrieve JSON data.

BCO-DMO

The BCO-DMO project metadata must be acquired manually and placed into the bco_dmo/tmp/bco_dmo.json directory.

NSF

This service scans through the database and queries the NSF API for award metadata.

DMPTool

This service scans through the database and queries the DMPTool for DMP metadata.

Standardized JSON Output

All of the services produce a standard JSON output:

{
  "projects": [
    {
      "identifiers": ["99999", "ABCD"],
      "types": ["Creative Work", "http://url.to.my/controlled/vocabulary/page"],
      "title": "Sample Project",
      "description": "This is a description of our important project",
      "license": "MIT",
      "publication_date": "2018-01-01",
      "language": "en",

      "markers": [
        {
          "uri": "",
          "value": "MS-A",
          "defined_by": "",
          "definition": "mitochondrial sub-unit A"
        },
        {
          "uri": "http://controlled.vocab.org/test",
          "value": "ABC",
          "defined_by": "creator name",
          "definition": "species ABC"
        }
      ],

      "contributors": [
        {
          "name": "John Doe",
          "email": "john.doe@nowhere.org",
          "role": "Principal Investigator",
          "org": {
            "types": ["Institution"],
            "identifiers": ["UONW"],
            "name": "University of Nowhere"
          }
        }
      ],

      "awards": [
        {
          "name": "ABCD-1234 Semi-Annual for exceptional research topics",
          "identifiers": ["ABCD-1234", "http://url.to.my/awards/landing/page"],
          "org": {
            "types": ["Organization"],
            "identifiers": ["http://link.to.an/org/page"],
            "name": "Funder Institution"
          },
          "offered_by": {
            "name": "Dr. Funder Person",
            "identifiers": ["http://link.to.an/user/landing/page"],
            "role": "Program Manager"
          }
        }
      ],

      "documents": [
        {
          "identifiers": ["https://dmptool.org/path/to/dmp.pdf"],
          "types": ["Data Management Plan", "application/pdf"],
          "title": "Data Management Plan"
        }
      ],
      
      "stages": [
        {
          "identifiers": ["12389", "TEST 1"],
          "types": ["Cruise"],
          "title": "TEST 1 spreadsheet dataset",
          "start_date": "2018-06-21 08:09:10",
          "contributors": [
            {
              "identifiers": ["0"],
              "name": "demo",
              "role": "Co-principal Investigator"
            }
          ],
          "public": "true"
        }
      ]
    }
  ],
}

SQL Database

There is a MySQL database definition in sql_database/maDMPs.sql which can be used to generate your DB. Once your DB has been created you can run ruby application.rb to populate it.

• To run all services and load their findings into the DB run ruby application.rb.
• To run a specific service(s) and load its findings into the DB just supply the name(s) of the services you want to run: ruby application service1 service2

The available services are: biocode, geome, bco_dmo, nsf, dmptool