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Re: BioSamples type for review

From: Carl Boettiger <cboettig@gmail.com>
Date: Mon, 20 May 2019 12:39:55 -0700
Message-ID: <CAN_1p9x5MYfusxt-jVV3J7XOwVNjHKgDFtrFoxXwT0+bKjiNVw@mail.gmail.com>
To: Chris Mungall <cjmungall@lbl.gov>
Cc: Matt Styles <Matt.Styles@nottingham.ac.uk>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Thanks Chris.  Just chiming in here as one such observer, I share your
impression here.
---
Carl Boettiger
http://carlboettiger.info/


On Mon, May 20, 2019 at 11:56 AM Chris Mungall <cjmungall@lbl.gov> wrote:

> 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*
>>
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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
>>
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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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>> +44 (0) 115 74 85125 *| *nottingham.ac.uk
>>
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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
>>
>>
>>
>> To arrange a meeting: http://doodle.com/ajggray
>>
>>
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Received on Monday, 20 May 2019 19:40:34 UTC

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