Re: BioSamples type for review

Prior to this I started on a document that compares different
representations of samples across different schemas and domains, here it is
if it's useful for the bioschemas effort:
https://docs.google.com/document/d/1ExjXV5Y42SwH18cV91C9NbWkHooNjPpwL960lbT6eZ4/edit#

On Mon, May 13, 2019 at 8:26 AM Chris Mungall <cjmungall@lbl.gov> wrote:

>
>
> 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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