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BioSampleCodingNotes.md

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Proposal of BioSample Type

The Bioschemas community would like to propose a new type for marking up details of biological samples such as those found in bio banks, museums, and herbaria.

Background

The BioSample type has been discussed in the Bioschemas community in:

The proposal is an evolution of an earlier prototype of a Sample type developed for exchanging data about samples and deployed on the EBI BioSamples archive.

Proposal

The proposed type is available at http://sdo-bioschemas-227516.appspot.com/BioSample (a cached copy is also available on the Bioschemas website).

We summarise here the design decisions taken to reach this proposal.

Type Hierarchy

We are proposing to add the BioSample type under a BioChemEntity type which inherits from schema:Thing. BioChemEntity is being proposed as an umbrella type that the various types coming from Bioschemas will be placed under. This is to prevent bloat at the top level of Schema.org. BioSample will reuse some of the properties from BioChemEntity, e.g. associatedDisease and taxonomicRange.

An alternative would be for there to be a more generic Sample type in Schema.org with BioSample being a child. You could imagine there being a need to markup a sample of a product for sale which would have a different emphasis from a BioSample. Similarly, there have been discussions with the Bioschemas community about the need for a GeoSample that would include spatial properties, or StatisticalSample, but we have not worked on either of these. If this approach is favoured by the Schema.org community, then the associatedDisease and taxonomicRange properties would need their definitions extended, unless a multi-inheritance of Sample and BioChemEntity is used.

Properties

  • additionalProperty: Range extended to include BioSample.
  • collector: New property Considered creditedTo but felt that the two were distinct from each other in their intended use.
    There are also distinct uses of these terms to refer to different entities, i.e. who collected the sample versus who it is credited to.
  • custodian: New property Considered accountablePerson but range only permitted schema:Person. The custodian of a sample is often an schema:Organization.
  • dateCreated: Range extended to include BioSample.
    Potential issue is that the description of dateCreated mentions CreativeWork which BioSample does not inherit from.
  • gender: Range extended to include BioSample.
  • isControl: New property
  • itemLocation Range extended to include BioSample.
  • locationCreated Range extended to include BioSample.
    Potential issue is that the description of locationCreated mentions CreativeWork which BioSample does not inherit from.
  • samplingAge: New property Considered age but felt that was too generic, particularly with the proposed description of the property.