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Fwd: BioSamples type for review

From: Michael Baudis <mbaudis@me.com>
Date: Mon, 13 May 2019 17:20:58 +0200
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
To: Chris Mungall <cjmungall@lbl.gov>, "Gray, Alasdair J G" <a.j.g.gray@hw.ac.uk>
Message-Id: <2DB39310-6A50-4D2B-A6AD-6C610F49AE58@me.com>
Hi all,

would it make sense to align this between Phenopackets <-> bioschemas <-> schemablocks.org <http://schemablocks.org/> (well, I think it would, to a degree)?

- we are aware that geolocation data has to be provided, but not exactly about the extend (we think more about it in terms of “provenance”, not in a “where the hell is the sample stored”, which is outside of a data model’s scope, IMO)
- for material, with a focus on biomedical samples, we started to use new EFO classes w/ a target of “is this a sample representing the individual, or some abnormal part” (not yet in the schema)
- etc.

SchemaBlocks aligns (bi-directional) w/ Phenopackets, but tries to represent a larger set of scenarios. So any common parts (e.g. the format of geo data, if not the scoping) could be harmonised.

Michael.



	"provenance" : {
		"material" : {
			"type" : {
				"id" : "EFO:0009656",
				"label" : "neoplastic sample"
			}
		},
		"geo" : {
			"label" : "Antalya, Turkey",
			"precision" : "city",
			"city" : "Antalya",
			"country" : "Turkey",
			"latitude" : 36.91,
			"longitude" : 30.7
		}
	}



> On 13 May 2019, at 17:06, Matt Styles <Matt.Styles@nottingham.ac.uk <mailto: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.
> 
> 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.
> 
> 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 <mailto:cjmungall@lbl.gov>>
> Sent: Monday, May 13, 2019 3:51:14 PM
> To: Gray, Alasdair J G
> Cc: public-bioschemas@w3.org <mailto: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 <http://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 <mailto: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 <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 <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 <http://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 <mailto:A.J.G.Gray@hw.ac.uk>
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> ORCID: http://orcid.org/0000-0002-5711-4872 <http://orcid.org/0000-0002-5711-4872>
> Office: Earl Mountbatten Building 1.39
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> 
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Received on Monday, 13 May 2019 15:23:35 UTC

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