Re: BioSamples type for review

On Mon, May 20, 2019 at 8:57 AM Matt Styles <Matt.Styles@nottingham.ac.uk>
wrote:

> Do you have some examples?
>

https://gold.jgi.doe.gov/biosamples?Biosample.Ecosystem=Environmental&Biosample.Specimen=biome&Biosample.Is+Public=Yes
https://www.ebi.ac.uk/metagenomics/search#samples


>
>
> It was a face-to-face meeting.
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>
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> *Matt Styles*
>
> *Senior Research Developer*
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> *From:* Chris Mungall <cjmungall@lbl.gov>
> *Sent:* 20 May 2019 16:49
> *To:* Matt Styles <uczms@exmail.nottingham.ac.uk>
> *Cc:* Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>; public-bioschemas@w3.org
> *Subject:* Re: BioSamples type for review
>
>
>
> Hi Matt,
>
>
>
> Did you discuss environmental biosamples? I agree plant and animal
> biosample would be similar and I would not propose making separate
> subclasses here. But environmental biosamples may have vastly different
> properties.
>
>
>
> When you say the general consensus, was this a discussion on github or a
> telecon? How does one get involved in guiding the general consensus?
>
>
>
> On Mon, May 20, 2019 at 7:13 AM Matt Styles <Matt.Styles@nottingham.ac.uk>
> wrote:
>
> Yes, thinking about this structure..
>
>
>
> The general consensus of us discussing the BioSample type was that it
> would be a child of BioChemEntity.
>
>
>
> I think, though open to thoughts, is that over time there may be a need
> for a general Sample type, but presumably this wouldn’t be difficult to add
> retrospectively because it would only add properties to, rather than modify
> existing properties of, BioSample (GeoSample, etc). The ‘open-closed
> principle’ of software development.
>
>
>
> We discussed the difference between e.g. PlantSample vs HumanSample (for
> example), but pretty much all the properties we came up with applied
> equally to both, hence keeping it simple (KISS!) with BioSample.
>
>
>
> Hope this gives some context to how the proposals evolved..
>
>
>
> Thanks,
>
>
>
> Matt
>
>
>
> *Matt Styles*
>
> *Senior Research Developer*
>
>
>
> Suite 221 46 Eversholt Street,
>
> Euston,
>
> London,
>
> NW1 1DA
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> *From:* Chris Mungall <cjmungall@lbl.gov>
> *Sent:* 17 May 2019 23:55
> *To:* Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
> *Cc:* Matt Styles <uczms@exmail.nottingham.ac.uk>;
> public-bioschemas@w3.org
> *Subject:* Re: BioSamples type for review
>
>
>
> Comments below..
>
>
>
> On Wed, May 15, 2019 at 2:55 AM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
> wrote:
>
> 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
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> To arrange a meeting: http://doodle.com/ajggray
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