schema.org and biomedical ontologies
TRANSCRIPT
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Microdata and ontologies
Simon Jupp and Tony BurdettSamples, Phenotypes and Ontologies TeamThe European Bioinformatics Institute
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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
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<a href=http://www.ebi.ac.uk/efo/EFO_0000400>diabetic</a>
Ontology concept
Ontology terms sometimes hyperlinked
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Ontology Lookup Service• http://www.ebi.ac.uk/ols/beta/ • 140 biomedical ontologies• 3.4 million terms• 11 million relationships
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Connecting ontologies to the data
Data Terms Ontology
Defined byisAbout
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Connecting ontologies to the data
Biosamples entry(Diabetic mouse strain)
Diabetes termEFO_0000400 Experimental
Factor Ontology
Defined byisAbout
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Schema.org properties for ontology terms
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Ontology term = vocab:MedicalCode
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Ontology term = vocab:MedicalCode
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Ontology = vocab:CreativeWork
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Ontology = vocab:CreativeWork
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Biosamples page = vocab:MedicalEntity
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Biosamples page = vocab:MedicalEntity
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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
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Using Schema.org to connect these resources
What ontologies are used in <my data>?
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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
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Using Schema.org to connect these resources
What is <my data> broadly about?
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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
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Using Schema.org to connect these resources
Which databases are using <my ontology>?
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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
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Using Schema.org to connect these resources
Can I use an ontology to enrich the search over <my data>?
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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
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Google custom search engine over vocab:MedicalCode
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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
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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?