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Re: BioSamples type for review

From: Matt Styles <Matt.Styles@nottingham.ac.uk>
Date: Mon, 13 May 2019 15:06:19 +0000
To: "Gray, Alasdair J G" <a.j.g.gray@hw.ac.uk>, Chris Mungall <cjmungall@lbl.gov>
CC: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <AM6PR06MB5473CF48644688E15A1A11B0AB0F0@AM6PR06MB5473.eurprd06.prod.outlook.com>
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

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________________________________
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<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

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<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>
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 15:06:48 UTC

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