7.8.3. Data catalogue markup




Recipe Overview
Reading Time
10 minutes
Executable Code
No
Difficulty
Data catalogue markup
FAIRPlus logo
Recipe Type
Guidance
Audience
Software Developer, Data Scientist

7.8.3.1. Main Objectives

The main purpose of this recipe is:

To embed Schema.org markup in a web page that publishes multiple datasets in a single page.


7.8.3.2. Graphical Overview

The process of annotating a data catalog webpage with bioschema markup for Search Engine discovery

Fig. 7.9 The process of annotating a data catalog webpage with bioschema markup for Search Engine discovery.


7.8.3.3. Capability & Maturity Table

Capability

Initial Maturity Level

Final Maturity Level

Findability

minimal

repeatable

Interoperability

minimal


7.8.3.4. Method

We will outline the steps for marking up a page in your site that is about multiple datasets. The resulting markup will be compliant with both Google’s Dataset markup guidelines and the Bioschemas DataCatalog Profile.

We will use FAIRsharing as an example for this recipe which makes three datasets available within its markup.

  1. Identify the page in your site about a specific dataset, e.g. https://fairsharing.org/

  2. Open the Bioschemas Generator

    1. Select DataCatalog from the Bioschemas Profile dropdown

    2. Enter the URL of the page in URL box, e.g. https://fairsharing.org/

    3. Click on the Show Form button

Bioschemas Generator start screen.

Fig. 7.10 Bioschemas Generator start screen.

  1. Complete the profile form with the information relevant for your page. Once completed, click on the Generate Markup button

    • You should complete all Minimum properties and as many Recommended properties as possible. You can show/hide properties using the Additional Properties buttons.

    • Where possible you should link to other resources. The Bioschemas Generator does not make this as simple as it could, but you can do it in step 5 once you have generated your markup, e.g. our dataset will link to a page with DataCatalog markup in rather than repeating all the properties for now we will just enter a url and no other properties.

      • If there are separate pages for your datasets then you should link to them using an @id link

      • Otherwise you can include the markup within the DataCatalog markup

    • The form defaults to the data type with the first alphabetical character, e.g. for identifier this defaults to PropertyValue but Text or URL will be more appropriate in most cases

    • The right side of the screen gives examples for properties, where these have been provided by the Bioschemas profile authors. Click on the Show button to see the example for a specific property. Click on Minimum, Recommended, or Optional to expand/contract the section and see the properties contained at that marginality level

Bioschemas Generator DataCatalog profile form

Fig. 7.11 Bioschemas Generator DataCatalog profile form.

  1. You will now see the generated markup in JSON-LD format. You can click on the Microdata and RDFa tabs to see the same content rendered in the different formats. However, we recommend the use of JSON-LD. For our FAIRsharing.org example, we get the following markup

    <script type="application/ld+json" >
    {
      "@context": "http://schema.org",
      "@id": "https://fairsharing.org/",
      "@type": "DataCatalog",
      "alternateName": [
        "BioSharing.org"
      ],
      "citation": [
        {
          "@id": "https://doi.org/10.1038/s41587-019-0080-8",
          "@type": "CreativeWork"
        }
      ],
      "dataset": [
        {
          "@context": "http://schema.org",
          "@type": "Dataset",
          "dct:conformsTo": "https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14",
          "description": "A manually curated registry of standards, split into three types - Terminology Artifacts (ontologies, e.g. Gene Ontology), Models and Formats (conceptual schema, formats, data models, e.g. FASTA), and Reporting Guidelines (e.g. the ARRIVE guidelines for in vivo animal testing). These are linked to the databases that implement them and the funder and journal publisher data policies that recommend or endorse their use.",
          "identifier": [
            "https://www.fairsharing.org/bsg-sXXXXXX"
          ],
          "keywords": [
            "Standards",
            "Metadata",
            "Formats",
            "Ontologies",
            "Terminology Artifacts",
            "Reporting Guidelines"
          ],
          "name": "Metadata Standard",
          "url": "https://fairsharing.org/standards"
        },
        {
          "@context": "http://schema.org",
          "@type": "Dataset",
          "dct:conformsTo": "https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14",
          "description": "A manually curated registry of databases/data repositories, conforming to the BioDBcore standard (from the Life Sciences). These are linked to the standards that they use and the funder and journal publisher data policies that recommend or endorse their use.",
          "identifier": [
            "https://www.fairsharing.org/bsg-dXXXXXX"
          ],
          "keywords": [
            "Database",
            "Data repository"
          ],
          "name": "Database",
          "url": "https://fairsharing.org/databases"
        },
        {
          "@context": "http://schema.org",
          "@type": "Dataset",
          "dct:conformsTo": "https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14",
          "description": "A manually curated registry of data policies from research funders, journal publishers, societies, and other organisations. These are linked to the databases and standards that they recommend for use",
          "identifier": [
            "https://www.fairsharing.org/bsg-pXXXXXX"
          ],
          "keywords": [
            "Data policy",
            "journal",
            "funder",
            "society"
          ],
          "name": "Data Policy",
          "url": "https://fairsharing.org/policies"
        }
      ],
      "dct:conformsTo": "https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01",
      "description": "A manually curated, informative and educational resource on data and metadata standards, inter-related to databases/data repositories and funder and journal publisher data policies from across disciplines. FAIRsharing is an ELIXIR-UK node resource and has an active role in the RDA and Force11 data initiatives.",
      "identifier": [
        "https://identifiers.org/MIR:00000364"
      ],
      "keywords": [
        "registry",
        "life science",
        "natural science",
        "social science"
      ],
      "license": {
        "@id": "https://creativecommons.org/licenses/by-sa/4.0/",
        "@type": "CreativeWork"
      },
      "name": "FAIRsharing.org",
      "provider": [
        {
          "@context": "http://schema.org",
          "@type": "Organization",
          "dct:conformsTo": "https://bioschemas.org/profiles/Organization/0.2-DRAFT-2019_07_19",
          "description": "",
          "name": "FAIRsharing.org Registry"
        }
      ],
      "url": "https://fairsharing.org/"
    }
    </script >
    
  2. Download or copy and paste the generated markup

  3. Make adjustments for any bits that could not be properly entered through the form.

    For example, for our generated markup we would change the provider so that it provides a direct link rather than repeating the properties. We would replace

    "provider": [
        {
          "@context": "http://schema.org",
          "@type": "Organization",
          "dct:conformsTo": "https://bioschemas.org/profiles/Organization/0.2-DRAFT-2019_07_19",
          "description": "",
          "name": "FAIRsharing.org Registry"
        }
      ],
    

    with

    "provider": [
        {
          "@type": "Organization",
          "@id": "https://fairsharing.org/communities"
        }
      ],
    

    You can test that your JSON-LD is valid syntax, and visualise your markup using the JSON-LD Playground.

  4. Once you are happy with your markup, include the JSON-LD, script tags and all, at the bottom of your HTML page template. Make sure that this is before the closing </html> tag

Your site should now include DataCatalog markup.

Once you have deployed this on your web server, you can test it with the Bioschemas Validator which scrapes the markup from your page and allows you to test it against various Bioschemas profiles1.


7.8.3.5. FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks

Input

Output

text annotation

Bioschemas

annotated text

validation

schema.org

report

7.8.3.6. Table of Data Standards

Data Formats

Terminologies

Models

JSON-LD

Bioschemas

RDF

HTML


7.8.3.7. Authors

Name

ORCID

Affiliation

Type

ELIXIR Node

Contribution

Heriot Watt University

Writing - Original Draft

ZB MED Information Centre for life sciences

Writing - Review & Editing

University of Oxford

Writing - Review & Editing


7.8.3.8. Footnotes

1: The Bioschemas Validator is currently in an early alpha release and does not include all the profiles.


7.8.3.9. License

This page is released under the Creative Commons 4.0 BY license.