Exploring existing schema.org vocabulary for adding structured data markup to ontology terms

1. Microdata and ontologies
Simon Jupp and Tony Burdett
Samples, Phenotypes and Ontologies Team
The European Bioinformatics Institute

2. Ontologies in the life sciences
• Life sciences been quick to adopt ontologies for
annotation of data
• Over 200 biomedical ontologies in active use
• Large amount of data at EMBL-EBI annotated to
ontologies
• A lot of it still hidden in backend databases
• Rarely exposed in a structured way

3. <a href=http://www.ebi.ac.uk/efo/EFO_0000400>diabetic</a>
Ontology concept
Ontology terms sometimes hyperlinked

4. Ontology Lookup Service
• http://www.ebi.ac.uk/ols/beta/
• 140 biomedical ontologies
• 3.4 million terms
• 11 million relationships

5. Connecting ontologies to the data
Data
Terms Ontology
Defined byisAbout

6. Connecting ontologies to the data
Biosamples entry
(Diabetic mouse strain)
Diabetes term
EFO_0000400
Experimental
Factor
Ontology
Defined byisAbout

7. Schema.org properties for ontology terms

8. Ontology term = vocab:MedicalCode

9. Ontology term = vocab:MedicalCode

10. Ontology = vocab:CreativeWork

11. Ontology = vocab:CreativeWork

12. Biosamples page = vocab:MedicalEntity

13. Biosamples page = vocab:MedicalEntity

14. Using Schema.org to connect these
resources
Organization
- name
MedicalEntity
- name
- description
MedicalCode
- codeValue
…
MedicalCode
- name
- url
- alternateName
- description
- codeValue
- codingSystem
…
CreativeWork
- about
- name
- description
- url
- datePublished
…
Data Term Ontology

15. Using Schema.org to connect these
resources
What ontologies are used in <my data>?

16. Using Schema.org to connect these
resources
Organization
- name
MedicalEntity
- name
- description
MedicalCode
- codeValue
MedicalCode
- name
- url
- alternateName
- description
- codeValue
- codingSystem
…
CreativeWork
- about
- name
- description
- url
- datePublished
…
Data Term Ontology

17. Using Schema.org to connect these
resources
What is <my data> broadly about?

18. What is the biosamples page about?
Organization
- name
MedicalEntity
- name
- description
MedicalCode
- codeValue
MedicalCode
- name
- url
- alternateName
- description
- codeValue
- codingSystem
…
CreativeWork
- about (disease)
- name
- description
- url
- datePublished
…
Data Term Ontology

19. Using Schema.org to connect these
resources
Which databases are using <my ontology>?

20. Where is an ontology/term being used?
Organization
- name
MedicalEntity
- name
- description
MedicalCode
- codeValue
- codingSystem
MedicalCode
- name
- url
- alternateName
- description
- codeValue
- codingSystem
…
CreativeWork
- about
- name
- description
- url
- datePublished
…
Data Term Ontology

21. Using Schema.org to connect these
resources
Can I use an ontology to enrich the search over <my data>?

22. Enriching content
Organization
- name
MedicalEntity
- name
- description
MedicalCode
- codeValue
- codingSystem
MedicalCode
- name
- url
- alternateName
- description
- codeValue
- codingSystem
…
CreativeWork
- about
- name
- description
- url
- datePublished
…
Data Term Ontology

23. Google custom search engine over
vocab:MedicalCode

24. Schema.org questions
• MedicalEntity / MedicalCode too narrow
• We have plants and other non-medical entities
• Ontology/Terminology as a CreativeWork?
• Where does schema.org stop?
• AnatomicalStructure > Bone, Nerve, Muscle seem very
specific

25. What next
• Develop patterns and best practice for schema.org
markup for data + ontology
• Pilot to add markup to Biosamples and GWAS website
• Develop more use cases
• How to exploit Google CSE
• What would a rich snippets for data + ontology look like?