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

Re: BioSamples type for review

From: Chris Mungall <cjmungall@lbl.gov>
Date: Mon, 13 May 2019 08:26:19 -0700
Message-ID: <CAN9Aifvn31qOO83MfzPZtX7eviVqoBhJxETJzJDMkny6+kGS9Q@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>
On Mon, May 13, 2019 at 8:06 AM Matt Styles <Matt.Styles@nottingham.ac.uk>
wrote:

> Mix.
>
> The problem with just using additional property for everything is that we
> are pretending to define a scheme without actually defining a schema. We
> are proposing to retain this in BioSample for backwards compatibility but
> it isn't much if a schema.
>

agreed, but it seems unlikely you will manage to enumerate all possible
properties. I don't know enough about the context of bioschemes to say if
this is a problem. E.g in an open world rdf/json-ld it's always possible to
make additional triples, but if it's to be used like json-schema then this
could be restrictive.


> 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)


>
> I think if we try to hard to cover all bases them we will struggle to get
> live implementations, which is the real value, so it is a balancing act.
>
> Matt
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------------------------------
> *From:* Chris Mungall <cjmungall@lbl.gov>
> *Sent:* Monday, May 13, 2019 3:51:14 PM
> *To:* Gray, Alasdair J G
> *Cc:* public-bioschemas@w3.org
> *Subject:* Re: BioSamples type for review
>
> Hi all,
>
> What is the scope of BioSample?
>
> It seems that if one of the goals is to get incorporated into the main
> schema.org then it may be possible to generalize to include e.g.
> geological samples.
>
> Keeping just within the bio scope, it seems that the main use case for
> this is biomedical samples, yet ncbi/ebi biosamples includes environmental
> samples? Has there been any attempt to align with MIxS?
>
> I recall a previous version of BioSample that allowed arbitrary sets of
> property values for a sample. This had the disadvantage of having no way of
> constraining the set of properties but had the advantage of being able to
> represent anything in MIxS
>
> Some specific comments on individual fields:
>
> Is location the location of the sample source or where the sample is
> stored? Important to have clear semantics for this for environmental
> samples.
>
> The material field seems a bit odd "A material that something is made
> from, e.g. leather, wool, cotton, paper."
>
> I don't understand how these fields are intended to be used:
> bioChemInteraction, bioChemSimilarity, hasMolecularFunction, [most of them]
>
>
>
> On Mon, May 13, 2019 at 1:53 AM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
> wrote:
>
>> Hi All
>>
>>
>> One of the outcomes of last week’s meeting was for a revised proposal of
>> the Sample type, now renamed to BioSample and nested under BioChemEntity.
>>
>> I have now updated the type definition which can be found at
>> http://bio.sdo-bioschemas-227516.appspot.com/BioSample
>>
>> A GitHub issue has been created for this proposal. Please review the
>> issue and add comments there.
>>
>> https://github.com/BioSchemas/specifications/issues/306
>>
>> The most recent comment identifies a few outstanding issues that need to
>> be resolved.
>>
>>
>>    -  BioSample type definition updated to reflect that it only relates
>>    to bio samples. Please review.
>>    -  New proposal for collector is probably far enough away from the
>>    existing creditedTo <https://schema.org/creditedTo> property that we
>>    keep it as a separate property
>>    -  New proposal for custodian property: could the existing
>>    accountablePerson <https://schema.org/accountablePerson> be used
>>    instead. It might need a tweak of the definition
>>    -  Existing dateCreated <https://schema.org/dateCreated> property
>>    mentions CreativeWork in its description. We probably need that to be
>>    updated in the schema.org definition.
>>    -  For geographicLocation I have added location
>>    <https://schema.org/location> and locationCreated
>>    <https://schema.org/locationCreated>.
>>       -  Instead of location <https://schema.org/location> would the
>>       more specific itemLocation <https://schema.org/itemLocation> make
>>       sense?
>>       -  The definition of locationCreated
>>       <https://schema.org/lcoationCreated> mentions CreativeWork so
>>       would need rephrasing
>>    -  Proposed phenotype property needs renaming so that it is not the
>>    same as the type (Phenotype). We also need a definition.
>>    -  Proposed pedigree property needs a definition and also expected
>>    types defined.
>>
>> We are keen to push this forward so that the BioBanks can finalise their
>> markup against this revised type.
>>
>> 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, 13 May 2019 15:26:59 UTC

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