A presentation of the bioschemas implementation in the EMBL-EBI Biosamples database presented at the Bioschemas adoption meeting on October 2nd 2017. Bioschemas is a proposed extension of Schema.org.

1. Bioschemas for Biosamples
Mélanie Courtot
GA4GH/Biosamples project lead
mcourtot@ebi.ac.uk
@mcourtot

2. BioSamples Database @ EBI

3. BioSamples connects across resources

4. Bioschemas Samples: use cases

5. Bioschemas Samples: milestones
• M1: Analysis and mapping of metadata already used in
existing sample registries and defined by existing standards
e.g. MIABIS
• M2: Define minimum information guidelines based on the
results of the mapping and feedback from registries
• Identify minimum set of properties
• M3: Test adoption and improve specification with selected
data repositories
• M4: Propose any new suggested types or properties to
schema.org

6. Bioschemas Samples: deliverables
• D1: Bioschemas specification
• D2: Data repository using Bioschemas compliant markup
• D3: Data registry using Bioschemas compliant markup

7. Bioschemas Samples: JSON export
"@context" : "http://schema.org",
"@type" : "BiologicalEntity",
"biologicalType" : "sample",
"identifier" : "SAMN04245817",
"name" : "Plant sample from Viridiplantae",
"url" : "http://www.ebi.ac.uk/biosamples/samples/SAMN04245817",
"datasetUrl" : [ "http://www.ebi.ac.uk/ena/data/view/SAMN04245817" ],
"additionalProperty" : [ {
"@type" : "PropertyValue",
"name" : "organism",
"value" : "Viridiplantae",
"code" : {
"@type" : "OntologyCode",
"url" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
}

8. Discussion point: OntologyCode
• Can we reuse existing?
• Currently
• additionalType
• Identifier
• MedicalCode

9. Working with other repositories: MarRef
https://mmp.sfb.uit.no

10. The road ahead
• Work with repositories/
Biobanks/LIMS to adopt
Bioschema
• Develop general crawler: in
collaboration with
Bioschema community

11. The EBI Biosamples team
Tony Burdett
Adam Faulconbridge
Luca Cherubin
Trish Whetzel
Matthew Green
Helen Parkinson