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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