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Re: BioSamples type for review

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Wed, 15 May 2019 09:55:23 +0000
To: Chris Mungall <cjmungall@lbl.gov>
CC: Matt Styles <Matt.Styles@nottingham.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <EF453CAF-B50A-421D-95BC-DE3CCCC44568@hw.ac.uk>

I think it is clear that we need to define some properties for BioSample rather than continue to rely on an approach that would permit anything. Although as Chris highlighted we are on the Web so anything goes, but let us try to provide a vocabulary of terms within schema.org<http://schema.org> that enable resources to become findable on the web.

On 13 May 2019, at 16:26, Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>> wrote:

If there is another type of sample which is not covered by BioSample then I think it would be worth considering, providing we have some examples that we could mark up today.

This goes back to my question about scope. If the scope is the same as ebi/ncbi biosamples and includes environmental samples then there is a lot missing.

If the scope is tissue samples from organisms then I recommend relabeling to make this clearer, but even here there are clear gaps, e.g. no way to indicate the tissue of origin e.g with an uberon ID.

To evaluate the list of properties I recommend looking at the relevant set of MIxS templates that are in scope (whether this is just biomedical or includes environmental)

The scope of the type is really up for discussion, but we need to decide on this soon. We would need to see a concrete example of what a GeoSample would be. Would it make sense to propose this as a sibling type to BioSample and have both inherit from a more generic Sample type, i.e.
- Sample
  - BioSample
  - GeoSample

This would also eliminate the inheritance of properties from the BioChemEntity type, although some of those were appropriate, e.g. associatedDisease.

Note that there is notion of sample in the existing Biomedical extension of schema.org<http://schema.org>. There are some specific types under MedicalTest that mention using a sample:

https://schema.org/PathologyTest which also has a property of tissueSample

We should also be aware that there is a property called sampleType, but this is defined in the context of a computer programme code sample with a more specific codeSampleType property as well.

On 13 May 2019, at 15:51, Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>> wrote:

Is location the location of the sample source or where the sample is stored? Important to have clear semantics for this for environmental samples.

I think we want to use itemLocation and locationCreated to make this distinction clear. These are both existing terms in schema.org<http://schema.org>.

On 13 May 2019, at 15:51, Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>> wrote:

The material field seems a bit odd "A material that something is made from, e.g. leather, wool, cotton, paper.”

What should we use instead?

On 13 May 2019, at 15:51, Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>> wrote:

I don't understand how these fields are intended to be used: bioChemInteraction, bioChemSimilarity, hasMolecularFunction, [most of them]

These are due to the inheritance from BioChemEntity which if we go with the type proposal above would not then come across. There were a few that were indicated as being needed, viz, associatedDisease, taxonimicRange. If we do keep BioSample inheriting from BioChemEntity, then the profile defined over it would make clear which of the properties are intended for use.

Best regards


Alasdair J G Gray
Associate Professor in Computer Science,
School of Mathematical and Computer Sciences
Heriot-Watt University, Edinburgh, UK.

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33

ORCID: http://orcid.org/0000-0002-5711-4872

Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair

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