W3C home > Mailing lists > Public > public-bioschemas@w3.org > May 2019

Re: BioSamples type for review

From: Chris Mungall <cjmungall@lbl.gov>
Date: Mon, 20 May 2019 13:59:36 -0700
Message-ID: <CAN9Aifug83wHoBMb_nXgNqcqx09XqdPm4vFYmVpbCQj6YJZyxA@mail.gmail.com>
To: Matt Styles <Matt.Styles@nottingham.ac.uk>
Cc: "Gray, Alasdair J G" <a.j.g.gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
I think there's something I'm not getting across here - my objection isn't
that biosample isn't applicable to plant samples (although it does seem
very human-centric, e.g. gender; how would we deal with hermaphroditic
plants, or a female flower from a hermaphrodicitic plant)

the objection is that it's misaligned to the microbiome use case where we
have a sample that consists of multiple microbes and environmental material
in some environmental context (which may itself involves other organisms,
e.g. plant roots).

I'm not really familiar with bioschemas profiles - looks to be synonymous
with class here: https://bioschemas.org/specifications/ -- are there
examples of how different communities could have different profiles for the
same class?

It's quite possible there is something I'm fundamentally misunderstanding
about bioschemas, sorry...


On Mon, May 20, 2019 at 12:48 PM Matt Styles <Matt.Styles@nottingham.ac.uk>
wrote:

> Other bio samples other than human samples were considered, e.g. plants.
>
Is there an example you could provide of an 'environmental sample' where
> BioSample would be completely incompatible?
>
> Not to say that we can't create sub types, but if we took trees or fossils
> as examples, the majority of BioSample properties apply, so we need to
> understand what other kinds of concrete biological samples exist where
> BioSample would be wholly incompatible.
>
> It is worth remembering that Types are different to Profiles.
>
> It is not uncommon for Types to have a large number of properties, so if
> there were other properties which would be applicable to some other
> (currently undefined) BioSample, they could be added. As with everything in
> schema.org, all properties of all Types are optional. If we consider the
> Location Type for example, all of the geo properties may be completely
> irrelevant to the body organ from which an animal tissue sample was taken.
>
> Profiles can be used by relevant communities to provide recommendations on
> which properties apply.
>
> This is already true in Bioschemas with a number of profiles being
> defined. So a human tissue community may define a Profile on top of the
> BioSample Type, which specifies which properties should be minimum,
> recommended, optional.
>
> The difficulty with sub typing is that it creates a lot of duplication,
> and we would also need proposals for these new types. In the case of plant
> and human and animal samples, all of the proposed BioSample properties
> apply so we would create three identical sub types.
>
> I think if we are going to consider this level of sub typing then we need
> concrete proposals for their properties and for each one we should have at
> least one live example somewhere on the web.
>
> Happy to hear thoughts..
>
> Matt
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> *From:* Chris Mungall <cjmungall@lbl.gov>
> *Sent:* Monday, May 20, 2019 6:55:33 PM
> *To:* Matt Styles
> *Cc:* Gray, Alasdair J G; public-bioschemas@w3.org
> *Subject:* Re: BioSamples type for review
>
> The general issue is that the existing schema is just a poor match for
> environmental samples. No "environment" property. Perhaps "material" is to
> be used for this? Properties that are inapplicable or confusing in the
> context of an environmental biosample. E.g. how would "age" be interpreted
> in for a soil sample?
> http://sdo-bioschemas-227516.appspot.com/BioSample
>
> I think the use cases driving the current design were clearly all from
> tissue sample perspective (here interpreting tissue as any piece of an
> organism), so we avoid problems by not claiming the broad name BioSample
> for a more specific use case, e.g. rename as TissueSample. This leaves open
> the possibility of an EnvironmentalBioSample at some future date with
> adequate representation from the necessary communities [I'm sure there are
> a few on this list but many may not be checking email as they are at GSC
> this week], and also the possibility of creating a broader BioSample
> grouping class.
>
> On Mon, May 20, 2019 at 9:55 AM Matt Styles < Matt.Styles@nottingham.ac.uk>
> wrote:
>
> Sorry, examples of properties you were referring to which would be
> problematic?
>
> *Matt Styles*
> *Senior Research Developer*
>
> Suite 221 46 Eversholt Street,
> Euston,
> London,
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> *From:* Chris Mungall <cjmungall@lbl.gov>
> *Sent:* 20 May 2019 17:36
> *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
>
>
>
> 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.
>
> *Matt Styles*
> *Senior Research Developer*
>
> Suite 221 46 Eversholt Street,
> Euston,
> London,
> NW1 1DA
>
> +44 (0) 115 74 85125 *| *nottingham.ac.uk
>
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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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>
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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.
>
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>
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