Bioschemas for Biosamples

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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.

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

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

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

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

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

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

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

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