[ODINAFRICA] connect the new Vessels database as an ODIS node

[jmckenna]

• Globefinity/Chris/@dilianadineva to develop new vessels database & search tool
• need guidance for generating required JSON-LD and sitemap
• cc @fils @pbuttigieg

[jmckenna]

Updates from 2022-11-03 meeting

• Globefinity is working on new search interface for ODINAFRICA, to query for projects, vessels, etc.
• @dilianadineva showed sample JSON generated for vessels:
  • https://ioc-africa.org/test/researchVesselsJSON.php

    {
    "vessel_id": "1",
    "vessel_name": "R.V Tafi",
    "country_id": "10",
    "ownership": "Kenya",
    "website_link": "link",
    "dimensions": "9.4x2.4",
    "gross_tonnage": "54",
    "year_built": "67",
    "max_persons": "4",
    "max_scientists": null,
    "operational_status": "1",
    "home_port": "Mombasa",
    "research_equipment": ""https:\/\/www.kmfri.co.ke\/images\/kmfri\/photo-news.JPG https:\/\/www.kmfri.co.ke\/images\/kmfri\/mtafiti-2.JPG"",
    "photo_link": "",
    "vessel_history": "",
    "additional_info": ""
    }

• @jmckenna showed the schema.org validator tool: https://validator.schema.org/
• @pbuttigieg stated that next step should be that @fils, himself, jeff to create a template for Globefinity to use (similar to examples in https://book.oceaninfohub.org/thematics/vessels/README.html )
• @jmckenna explained the importance of leveraging a sitemap (to point to the JSON-LD / or point to the pages containing the JSON-LD) so that ODIS can harvest these (sitemaps are described in https://book.oceaninfohub.org/publishing/publishing.html )
• @jmckenna to share example sitemaps and JSON-LD pages

[jmckenna]

@dilianadineva / Chris:

• here is an example sitemap.xml, from the OBIS node:
  • https://obis.org/sitemap_datasets.xml
  • pick one of those urls, and then load it into the schema.org validator, to see the JSON-LD
  • such as https://validator.schema.org/#url=https%3A%2F%2Fobis.org%2Fdataset%2Fba32788a-2193-4fe9-b252-01822c3dc924
  • OBIS includes the JSON-LD inside the actual record page (so you can view-source on one page, such as https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924 and look for a section <script type="application/ld+json">
• or here is the JSON-LD as part of that record's page:

  {
  "@context": {
      "@vocab": "https://schema.org/"
  },
  "@type": "Dataset",
  "@id": "https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924",
  "name": "Classified benthic data for mesophotic organisms and substrates around the Lord Howe Island and Balls Pyramid shelves, southwest Pacific Ocean (2013)",
  "description": "This dataset contains classified benthic data from 2,668 still images collected using a towed underwater camera system around the Lord Howe Island and Balls Pyramid shelves. Underwater imagery were collected at 39 sites in depths ranging 6 m to 115 m from surveys aboard the RV Southern Surveyor in February 2013 and Lord Howe Island Marine Park vessel Tursiops in November 2013.\nThe data published here is the taxa classified to genus level or better. The original data has been classified using the Collaborative and Annotation Tools for Analysis of Marine Imagery and Video (CATAMI) classification scheme as a standard for scoring marine biota and physical characteristics from underwater imagery.",
  "url": "https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924",
  "sameAs": [
      "https://www.marine.csiro.au/ipt/resource?r=benthic_lord_howe_island"
  ],
  "license": "This work is licensed under a  Creative Commons Attribution (CC-BY) 4.0 License",
  "citation": "Linklater, Michelle (2018), “Classified benthic data for mesophotic organisms and substrates around the Lord Howe Island and Balls Pyramid shelves, southwest Pacific Ocean”, Mendeley Data, v1 http://dx.doi.org/10.17632/x8v7yxzxj9.1",
  "version": "2022-06-07T03:02:18.000Z",
  "keywords": [
      "Occurrence",
      "Observation",
      "Occurrence"
  ],
  "variableMeasured": [],
  "includedInDataCatalog": {
      "@id": "https://obis.org",
      "@type": "DataCatalog",
      "url": "https://obis.org"
  },
  "temporalCoverage": "2013/2013",
  "distribution": {
      "@type": "DataDownload",
      "contentUrl": "https://www.marine.csiro.au/ipt/archive.do?r=benthic_lord_howe_island",
      "encodingFormat": "application/zip"
  },
  "spatialCoverage": {
      "@type": "Place",
      "geo": {
          "@type": "GeoShape",
          "polygon": "158.9701 -31.86922,158.9701 -31.45291,159.32665 -31.45291,159.32665 -31.86922,158.9701 -31.86922"
      },
      "additionalProperty": {
          "@type": "PropertyValue",
          "propertyID": "http://dbpedia.org/resource/Spatial_reference_system",
          "value": "http://www.w3.org/2003/01/geo/wgs84_pos#lat_long"
      }
  },
  "provider": [
      {
          "@id": "https://oceanexpert.org/institution/20942",
          "@type": "Organization",
          "legalName": "CSIRO National Collections and Marine Infrastructure",
          "name": "CSIRO National Collections and Marine Infrastructure",
          "url": "https://oceanexpert.org/institution/20942"
      }
  ]
  }

Other notes:

• if you are generating JSON-LD files (as opposed to embedding the JSON-LD in the HTML page as above) then your sitemap should contain the urls to the individual JSON-LD files (likely with a .jsonld extension)

[dilianadineva]

@dilianadineva / Chris:

• here is an example sitemap.xml, from the OBIS node:

  • https://obis.org/sitemap_datasets.xml

  • pick one of those urls, and then load it into the schema.org validator, to see the JSON-LD

  • such as https://validator.schema.org/#url=https%3A%2F%2Fobis.org%2Fdataset%2Fba32788a-2193-4fe9-b252-01822c3dc924

  • OBIS includes the JSON-LD inside the actual record page (so you can view-source on one page, such as https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924 and look for a section <script type="application/ld+json">

• or here is the JSON-LD as part of that record's page:

{
    "@context": {
        "@vocab": "https://schema.org/"
    },
    "@type": "Dataset",
    "@id": "https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924",
    "name": "Classified benthic data for mesophotic organisms and substrates around the Lord Howe Island and Balls Pyramid shelves, southwest Pacific Ocean (2013)",
    "description": "This dataset contains classified benthic data from 2,668 still images collected using a towed underwater camera system around the Lord Howe Island and Balls Pyramid shelves. Underwater imagery were collected at 39 sites in depths ranging 6 m to 115 m from surveys aboard the RV Southern Surveyor in February 2013 and Lord Howe Island Marine Park vessel Tursiops in November 2013.\nThe data published here is the taxa classified to genus level or better. The original data has been classified using the Collaborative and Annotation Tools for Analysis of Marine Imagery and Video (CATAMI) classification scheme as a standard for scoring marine biota and physical characteristics from underwater imagery.",
    "url": "https://obis.org/dataset/ba32788a-2193-4fe9-b252-01822c3dc924",
    "sameAs": [
        "https://www.marine.csiro.au/ipt/resource?r=benthic_lord_howe_island"
    ],
    "license": "This work is licensed under a  Creative Commons Attribution (CC-BY) 4.0 License",
    "citation": "Linklater, Michelle (2018), “Classified benthic data for mesophotic organisms and substrates around the Lord Howe Island and Balls Pyramid shelves, southwest Pacific Ocean”, Mendeley Data, v1 http://dx.doi.org/10.17632/x8v7yxzxj9.1",
    "version": "2022-06-07T03:02:18.000Z",
    "keywords": [
        "Occurrence",
        "Observation",
        "Occurrence"
    ],
    "variableMeasured": [],
    "includedInDataCatalog": {
        "@id": "https://obis.org",
        "@type": "DataCatalog",
        "url": "https://obis.org"
    },
    "temporalCoverage": "2013/2013",
    "distribution": {
        "@type": "DataDownload",
        "contentUrl": "https://www.marine.csiro.au/ipt/archive.do?r=benthic_lord_howe_island",
        "encodingFormat": "application/zip"
    },
    "spatialCoverage": {
        "@type": "Place",
        "geo": {
            "@type": "GeoShape",
            "polygon": "158.9701 -31.86922,158.9701 -31.45291,159.32665 -31.45291,159.32665 -31.86922,158.9701 -31.86922"
        },
        "additionalProperty": {
            "@type": "PropertyValue",
            "propertyID": "http://dbpedia.org/resource/Spatial_reference_system",
            "value": "http://www.w3.org/2003/01/geo/wgs84_pos#lat_long"
        }
    },
    "provider": [
        {
            "@id": "https://oceanexpert.org/institution/20942",
            "@type": "Organization",
            "legalName": "CSIRO National Collections and Marine Infrastructure",
            "name": "CSIRO National Collections and Marine Infrastructure",
            "url": "https://oceanexpert.org/institution/20942"
        }
    ]
}

Other notes:

• if you are generating JSON-LD files (as opposed to embedding the JSON-LD in the HTML page as above) then your sitemap should contain the urls to the individual JSON-LD files (likely with a .jsonld extension)

I've created a main sitemap file: https://ioc-africa.org/sitemap.xml with an index to a dynamically generated sitemap https://ioc-africa.org/test2/research-vessels-sitemap.xml with links to pages that have JSON-LD Githubissues.

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