BioSample Profile 0.1-DRAFT

[AlasdairGray]

The following proposal for a BioSample profile was made at the 8 May 2019 F2F meeting.

Required

• Identifier
• name
• description

Recommended

Optional

• collector [the person or persons who created the sample]
• creationDate [the date the sample was created]
• geographicLocation [the location of origin of the sample] (type:Place)
• taxonomicRange [Text or URL or bioschemas:Taxon]
• material [https://schema.org/material - A material that something is made from, e.g. heart, stem cell, whole plant, soil…]
• age [how old the object was when sample was created]
• phenotype [range Text or URL or schema.org Phenotype]
• associatedDisease [the disease that is represented by the sample e.g. malaria, bowel cancer, coeliac disease, Creutzfeldt–Jakob disease, etc]
• gender = https://schema.org/gender
• pedigree
• isControl [A boolean (true/false) value. If true, this sample is being use as a normal control, often in combination with another sample]

[AlasdairGray]

Profile proposal needs to be updated to be inline with the discussion in #306 and the proposal being put forward to schema.org.

[mcourtot]

I didn't find a complete discussion around gender at https://github.com/BioSchemas/specifications/issues/306, but this seems wrong to me: gender is a social construct, I suspect we mean biological sex here?

[qgroom]

I didn't find a complete discussion around gender at #306, but this seems wrong to me: gender is a social construct, I suspect we mean biological sex here?

Yes, you are probably right.

[kcmcleod]

Current profile on gSheets: https://docs.google.com/spreadsheets/d/1LM7FaSJABWU5uG9ns9EU73HtHuV93hwB1m5LuKb4mEk/edit?usp=sharing

I suspect we mean biological sex here

Ignoring this in order to match proposal to schema.org

[petrospaps]

@AlasdairGray how do you define pedigree?

[AlasdairGray]

For now, only include the types that have been defined at https://bioschemas.org/types/BioSample/. The BioSamples group have for now decided not to include pedigree.

[kcmcleod]

https://docs.google.com/spreadsheets/d/1kcq7fEP1sQ9zf2YRNoyUYY87ahkz4ZsnRXHEb89KiOg

Updated this based on the above instructions and the type. Guessed cardinality & marginality values. I assume some CVs should be used, but these are not specified anywhere so leaving this blank.

[AlasdairGray]

Need to add cardinality restrictions