Microdata and ontologies Simon Jupp and Tony Burdett Samples, Phenotypes and Ontologies Team The European Bioinformatics Institute
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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
Ontology Lookup Service• http://www.ebi.ac.uk/ols/beta/ • 140 biomedical ontologies• 3.4 million terms• 11 million relationships
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 term = vocab:MedicalCode
Ontology = vocab:CreativeWork
Ontology = vocab:CreativeWork
Biosamples page = vocab:MedicalEntity
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
Using Schema.org to connect these resources
What ontologies are used in <my data>?
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
Using Schema.org to connect these resources
What is <my data> broadly about?
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
Using Schema.org to connect these resources
Which databases are using <my ontology>?
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
Using Schema.org to connect these resources
Can I use an ontology to enrich the search over <my data>?
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
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?
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