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Re: BioSamples type for review

From: Chris Mungall <cjmungall@lbl.gov>
Date: Fri, 17 May 2019 15:54:52 -0700
Message-ID: <CAN9AiftswLWt5Pkdk9tHQihxp+yU6SXUQRaTdAB+vF_jxMGXkw@mail.gmail.com>
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: Matt Styles <Matt.Styles@nottingham.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Comments below..

On Wed, May 15, 2019 at 2:55 AM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>

> Hi
> 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 that enable
> resources to become findable on the web.
> On 13 May 2019, at 16:26, Chris Mungall <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.
> Thing
> - Sample
>   - BioSample
>   - GeoSample
> This would also eliminate the inheritance of properties from the
> BioChemEntity type, although some of those were appropriate, e.g.
> associatedDisease.

I'm not sure of the philosophy of polymoprhism in schema.org other than
'keep it simple', but I think this approach would work best. Schema.org
does allow multiple inheritance so you could in theory have biosample
inherit from both sample and something like BioChemEntity, but AFAICT this
doesn't seem that common, and there seems to be a lack of trait/mixin
classes. Maybe some repetition of properties is fine.

How deep should the inheritance hierarchy go? I think subdividing biosample
into TissueSample and EnvironmentalBioSample would make sense as these will
have specific properties (although some overlap, in the case of
host-associated environmental samples).

You could go even further and subdivide environmental sample into the
different MIxS profiles (e.g SoilSample would have soil electroconductivity
property, depth property). This would have a lot of advantages but seems to
be not quite in the spirit of schema.org.

> Note that there is notion of sample in the existing Biomedical extension
> of schema.org. There are some specific types under MedicalTest that
> mention using a sample:
> https://schema.org/BloodTest
> https://schema.org/PathologyTest which also has a property of tissueSample

hmm, seems a bit ad-hoc

> 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.

also statistical samples. Maybe MaterialSample will help clarify this, at
the risk of sounding too ontological

> On 13 May 2019, at 15:51, Chris Mungall <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.
> On 13 May 2019, at 15:51, Chris Mungall <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> 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
> --
> 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 <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
> To arrange a meeting: http://doodle.com/ajggray
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Received on Friday, 17 May 2019 22:55:32 UTC

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