schema.org and biomedical ontologies

Microdata and ontologies

Simon Jupp and Tony BurdettSamples, Phenotypes and Ontologies TeamThe European Bioinformatics Institute

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

<a href=http://www.ebi.ac.uk/efo/EFO_0000400>diabetic</a>

Ontology concept

Ontology terms sometimes hyperlinked

http://www.ebi.ac.uk/efo/EFO_0000400



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

http://www.ebi.ac.uk/ols/beta/

http://www.ebi.ac.uk/ols/beta/

Connecting ontologies to the data

Data Terms Ontology

Defined byisAbout

Connecting ontologies to the data

Biosamples entry(Diabetic mouse strain)

Diabetes termEFO_0000400 Experimental

Factor Ontology

Defined byisAbout

Schema.org properties for ontology terms

Ontology term = vocab:MedicalCode

Ontology = vocab:CreativeWork

Biosamples page = vocab:MedicalEntity

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


What ontologies are used in <my data>?


Organization- name





Data Term Ontology


What is <my data> broadly about?

What is the biosamples page about?

Organization- name




CreativeWork- about (disease)- name- description- url- datePublished…

Data Term Ontology


Which databases are using <my ontology>?

Where is an ontology/term being used?

Organization- name


MedicalCode- codeValue- codingSystem



Data Term Ontology


Can I use an ontology to enrich the search over <my data>?

Enriching content

Organization- name


MedicalCode- codeValue- codingSystem



Data Term Ontology

Google custom search engine over vocab:MedicalCode

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

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?

schema.org and biomedical ontologies

Science

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