Tutorial given at European Open Science Cloud data interoperability workshop. The purpose was to evaluate whether schema.org markup could be used in a variety of scientific disciplines.

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3. Thing
Dataset
DataCatalog
BioChemEntity
LabProtocol
Data repositories, e.g.,
CreativeWork
includedInDataCatalog
Datasets and releases, e.g.,
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DataRecord
isPartOf
sample
reagent
mainEntity
mainEntityOfPage
hasPart

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8. Describes metadata for data
repositories and data catalogues
so they can be more easily
indexed by search engines and
registries.
Specification
Examples

9. →
{
"@context": "http://schema.org",
"@type": "DataCatalog",
"@id": "http://www.uniprot.org",
"name": "UniProt",
"description": "The Universal Protein Resource (UniProt) is a
comprehensive resource for protein sequence and annotation
data",
"url": "http://www.uniprot.org",
"keywords": "protein, protein sequence, protein annotation",
"provider": {
"@type": "Organization",
"name": "UniProt Consortium"
}
}

10. Describes metadata for datasets so
they can be more easily indexed by
search engines and registries.
Specification
Examples

11. →
{
"@type": "Dataset",
"@id": "http://www.uniprot.org/uniprot/",
"name": "UniProt Knowledgebase (UniProtKB)",
"description": "The UniProt Knowledgebase (UniProtKB) ...",
"url": "http://www.uniprot.org/uniprot/",
"identifier": "UniProtKB",
"keywords": "protein, protein sequence, protein annotations,
knowledgebase, TrEMBL, Swiss-Prot"
}

12. "includedInDataCatalog": "http://www.uniprot.org",
"creator": {
"@type": "Organization",
"name": "UniProt Consortium"
},
"version": "2017-09",
"license": "Creative Commons Attribution-NoDerivs",
"distribution": [
{
"@type": "DataDownload",
"name": "Reviewed (Swiss-Prot)",
"fileFormat": "xml",
"contentURL":
"ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uni
prot_sprot.xml.gz"
},
{
"@type": "DataDownload",
...
}
]
→

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15. {
"@context": "http://schema.org",
"@type": "BioChemEntity",
"additionalType": "http://semanticscience.org/resource/protein",
"identifier": "P00519",
"name": {
"@language": "en",
"@value": "ABL1"
},
"additionalProperty": {
"additionalType": "http://semanticscience.org/resource/is-transcribed-from",
"name": "gene",
"value": {
"@type": ["StructuredValue", "BioChemEntity"],
"additionalType": "http://semanticscience.org/resource/gene",
"identifier": "ABL1",
"name": "ABL1",
},
},
"isContainedIn": {
"@type": "BioChemEntity",
"additionalType": "http://semanticscience.org/resource/organism",
"identifier": "9606",
"name": "Homo sapiens",
"url": "http://purl.bioontology.org/ontology/NCBITAXON/9606"
}
}
→

16. →
"url": "http://www.uniprot.org/uniprot/P00519",
"additionalProperty": {
"additionalType": "http://semanticscience.org/resource/SIO_000983",
"name": "disease association",
"value": {
"@type": ["StructuredValue", "MedicalCondition"],
"additionalType": "http://semanticscience.org/resource/disease",
"name": "Leukemia, chronic myeloid (CML)",
"code": {
"@type": "MedicalCode",
"code": "608232",
"codingSystem": "OMIM"
},
"sameAs": "http://www.uniprot.org/diseases/DI-03735"
},
}

17. →
"alternateName": [
{
"@language": "en",
"@value": "ABL"
},
{
"@language": "en",
"@value": "JTK7"
}
],
"description": {
"@language": "en",
"@value": "Non-receptor tyrosine-protein kinase that plays a
role..."
}

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19. →
{
"@context": "http://schema.org",
"@type": "Record",
"@id": "http://www.identifiers.org/uniprot/P00519",
"identifier": "P00519",
"mainEntity": {...},
"isPartOf": {
"@type": "Dataset",
"@id": "http://www.uniprot.org/news/2017/03/15/release"
},
"additionalType": "http://purl.uniprot.org/core/Protein",
"url": "http://www.uniprot.org/uniprot/P00519",
}

20. "sameAs": "http://purl.uniprot.org/uniprot/P00519",
"citation": [
{
"@id": "http://www.identifiers.org/pubmed/10194451",
"@type": "ScholarlyArticle",
"name": { "@language": "en", "@value": "A novel SH2-containing ...“ },
"sameAs": [
"https://www.ncbi.nlm.nih.gov/pubmed/10194451", "http://europepmc.org/abstract/MED/10194451",
"http://purl.uniprot.org/citations/10194451"
]
},
{
"@id": "http://www.identifiers.org/pubmed/9037071",
"@type": "ScholarlyArticle",
"name": { "@language": "en", "@value": "Regulation of DNA ...“ },
"sameAs": [
"https://www.ncbi.nlm.nih.gov/pubmed/9037071", "http://europepmc.org/abstract/MED/9037071",
"http://purl.uniprot.org/citations/10194451"
]
}
],
"dateCreated": "1986-07-21",
"dateModified": "2017-03-15",
"distribution": {
"@type": "DataDownload",
"url": "http://www.uniprot.org/uniprot/P00519.fasta"
},
"seeAlso": [
"http://www.identifiers.org/pdb/1AB2", "http://www.identifiers.org/pdb/1ABL"
]
→

22. Examples & template
Creating your own DataCatalog
metadata
1. Copy the template.json example.
2. Change the values of the minimum fields.
3. Add as many recommended and optional fields as possible.
4. Wrap up the example using script tags.
<script type="application/ld+json">
....
</script>
5. Embed the example in your landing page.
• Name
• Description
• License
• Release
• Citation
• Metrics
• Tools
• …

23. Data Catalogue description for UniProt using
the minimum fields.
https://search.google.com/structured-data/testing-tool