9.9.1. Data page markup with Bioschemas¶

Recipe Overview

Reading Time

10 minutes

Executable Code

No

Difficulty

Data page markup with Bioschemas

Recipe Type

Guidance

Audience

Software Developer, Data Scientist

Maturity Level & Indicator

[F+MM-1.1C] [F+MM-1.2C]

Cite me with FCB011

9.9.1.1. Main Objectives¶

The main purpose of this recipe is:

To markup a webpage representing a data record with Bioschemas compliant markup.

9.9.1.2. Graphical Overview¶

9.9.1.3. Capability & Maturity Table¶

Capability	Initial Maturity Level	Final Maturity Level
Findability	minimal	repeatable
Interoperability	minimal

9.9.1.4. Method¶

We will outline the steps for embedding machine processable mark up within a web page in your site. As a specific example, we will use the Wikidata page for BRCA1.

Identify a data page in your site for which you will develop markup
Open the Bioschemas Generator
1. Select the type of data page that you are marking up, i.e. the primary subject of the page. In the example we will use Gene. Here are the Bioschemas profiles that you can choose from¹.
  - ChemicalSubstance for a page about a chemical substance composed of molecular entities
  - Gene for a page about a gene
  - MolecularEntity for a page about a single molecular entity
  - Protein for a page about a protein
  - BioSample for a page about a biological sample
  - Taxon for a page about a taxon
2. Enter the URL of the page in URL box, e.g. https://www.wikidata.org/wiki/Q227339. Note that this URL will be used as the identifier for the resource being described in the markup.
3. Click on the Show Form button

Complete the profile form with the data 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.
- 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

You should 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 Wikidata example, we get the following markup

<script type="application/ld+json" >
{
  "@context": "https://schema.org",
  "@id": "https://www.wikidata.org/wiki/Q227339",
  "@type": "Gene",
  "alternateName": [
    "breast cancer 1, early onset",
    "BRCAI",
    "BRCC1",
    "BROVCA1",
    "IRIS",
    "PNCA4",
    "PPP1R53",
    "PSCP",
    "RNF53",
    "FANCS",
    "breast cancer 1",
    "BRCA1, DNA repair associated",
    "BRCA1 DNA repair associated"
  ],
  "dct:conformsTo": "https://bioschemas.org/profiles/Gene/0.7-RELEASE",
  "description": "protein-coding gene in the species Homo sapiens",
  "encodesBioChemEntity": {
    "@type": "BioChemEntity",
    "@id": "https://www.wikidata.org/wiki/Q17487737"
  },
  "identifier": "https://www.wikidata.org/wiki/Q227339",
  "identifier": "Q227339",
  "image": {
    "@type": "ImageObject",
    "@id": "https://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Protein_BRCA1_PDB_1jm7.png/220px-Protein_BRCA1_PDB_1jm7.png"
  },
  "isPartOfBioChemEntity": {
    "@type": "BioChemEntity",
    "@id": "https://www.wikidata.org/wiki/Q220677"
  },
  "name": "BRCA1", 
  "sameAs": [
    "https://meshb.nlm.nih.gov/#/record/ui?ui=D019398",
    "https://www.ncbi.nlm.nih.gov/nuccore/NR_027676",
    "http://identifiers.org/ensembl/ENSG00000012048",
    "https://www.ncbi.nlm.nih.gov/gene/672",
    "http://identifiers.org/ncbigene/672"
  ],
  "taxonomicRange": {
    "@type": "Taxon",
    "@id": "https://www.wikidata.org/wiki/Q15978631"
  },
  "url": "https://www.wikidata.org/wiki/Q227339"
}
</script >

Download or copy and paste the generated markup
Make adjustments for any bits that could not be properly entered through the form.

For example, for our generated markup we would change

"encodesBioChemEntity": {
  "@type": "BioChemEntity",
  "@id": "https://www.wikidata.org/wiki/Q17487737"
},

to

"encodesBioChemEntity": {
  "@type": "Protein",
  "@id": "https://www.wikidata.org/wiki/Q17487737"
},

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

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
Replace the values in your markup with variables that your web page templating system will replace with values from your database. For example, the follow snippet uses variables of the form %%%PAGEURL%%%

<script type="application/ld+json" >
{
  "@context": "https://schema.org",
  "@id": "%%%PAGEURL%%%",
  "@type": "Gene",
  "dct:conformsTo": "https://bioschemas.org/profiles/Gene/0.7-RELEASE",
  "identifier": "%%%PAGEURL%%%",
  "description": "%%%DESCRIPTION%%%",
  ...
}

Your site should now generate data pages with embedded markup.

You should complete this process for each different type of data that you include in your site, e.g. ChEMBL would have MolecularEntity markup on their chemical pages and Protein markup on their target pages so would need to complete this process twice.

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 profiles².