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RE: BioSamples type for review

From: <frans@semantoya.nl>
Date: Fri, 7 Jun 2019 17:03:07 +0200
To: "'Gray, Alasdair J G'" <A.J.G.Gray@hw.ac.uk>, "'Chris Mungall'" <cjmungall@lbl.gov>
Cc: "'Matt Styles'" <Matt.Styles@nottingham.ac.uk>, <public-bioschemas@w3.org>
Message-ID: <018801d51d42$1f4cc6b0$5de65410$@semantoya.nl>
Dear All,

Unfortunately I was unable to attend the meeting at Schiphol due to consultation obligations,  though I would have liked to meet this highly appreciated community. Also due to oher professional obligations a somewhat delayed response. Sorry for that. 

Because nobody will know me,  please allow me to give a brief introduction. I’m  a clinical chemist and working at the department of clinical chemistry in one of the major medical laboratories in the NL. As a domain expert in medical diagnostics I’ve a special interest in the utilization of the Semantic Web technology to capture knowledge with (the digital knowledge twin). I understand the conceptual part of the technology, but frankly depend on others for the technical part.


Currentily I’m working on the preparations of a project (supported by my professional society) of which is the main goal to allow domain experts to construct high quality ontologies to harvest datasets 0f daily importance in an unambiguous and traceable manner.  Examples are the stability of biomarkers in matrices under different storage conditions, interferences of tests and reference values of biomarkers in given populations.  Such ontologies require a collaborative expertise of the domain experts. To avoid just another silo we want to explore the possibilities to reuse already existing definitions, taxonomies and ontologies.  Also we want to make a functional bridge between the medical laboratory professional and bio-informatics because the powerful concept of semantic web technology hasn’t penetrated our daily medical life community yet .


The concept of bioschema  fits in  this exploration how to collaborate and come up with some practical utilizations. Is there somebody with whom I can discuss these issues in more detail?

That would be great!


Best regards 


Frans van der Horst

Clinical chemist

Reinier Haga Medical Diagnostic Center

Delft NL









Van: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk> 
Verzonden: woensdag 15 mei 2019 11:55
Aan: Chris Mungall <cjmungall@lbl.gov>
CC: Matt Styles <Matt.Styles@nottingham.ac.uk>; public-bioschemas@w3.org
Onderwerp: Re: BioSamples type for review




I think it is clear that we need to define some properties for BioSample rather than continue to rely on an approach that would permit anything. Although as Chris highlighted we are on the Web so anything goes, but let us try to provide a vocabulary of terms within  <http://schema.org> schema.org that enable resources to become findable on the web.

On 13 May 2019, at 16:26, Chris Mungall < <mailto:cjmungall@lbl.gov> cjmungall@lbl.gov> wrote:



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)


The scope of the type is really up for discussion, but we need to decide on this soon. We would need to see a concrete example of what a GeoSample would be. Would it make sense to propose this as a sibling type to BioSample and have both inherit from a more generic Sample type, i.e.


- Sample

  - BioSample

  - GeoSample


This would also eliminate the inheritance of properties from the BioChemEntity type, although some of those were appropriate, e.g. associatedDisease.


Note that there is notion of sample in the existing Biomedical extension of  <http://schema.org> schema.org. There are some specific types under MedicalTest that mention using a sample:

 <https://schema.org/BloodTest> https://schema.org/BloodTest

 <https://schema.org/PathologyTest> https://schema.org/PathologyTest which also has a property of tissueSample


We should also be aware that there is a property called sampleType, but this is defined in the context of a computer programme code sample with a more specific codeSampleType property as well.


On 13 May 2019, at 15:51, Chris Mungall < <mailto:cjmungall@lbl.gov> cjmungall@lbl.gov> wrote:


Is location the location of the sample source or where the sample is stored? Important to have clear semantics for this for environmental samples.


I think we want to use itemLocation and locationCreated to make this distinction clear. These are both existing terms in  <http://schema.org> schema.org.


On 13 May 2019, at 15:51, Chris Mungall < <mailto:cjmungall@lbl.gov> cjmungall@lbl.gov> wrote:


The material field seems a bit odd "A material that something is made from, e.g. leather, wool, cotton, paper.”


What should we use instead?


On 13 May 2019, at 15:51, Chris Mungall < <mailto:cjmungall@lbl.gov> cjmungall@lbl.gov> wrote:


I don't understand how these fields are intended to be used: bioChemInteraction, bioChemSimilarity, hasMolecularFunction, [most of them]


These are due to the inheritance from BioChemEntity which if we go with the type proposal above would not then come across. There were a few that were indicated as being needed, viz, associatedDisease, taxonimicRange. If we do keep BioSample inheriting from BioChemEntity, then the profile defined over it would make clear which of the properties are intended for use.


Best regards





Alasdair J G Gray

Associate Professor in Computer Science, 
School of Mathematical and Computer Sciences 
Heriot-Watt University, Edinburgh, UK.

 <mailto:A.J.G.Gray@hw.ac.uk> Email: A.J.G.Gray@hw.ac.uk
Web:  <http://www.macs.hw.ac.uk/~ajg33> http://www.macs.hw.ac.uk/~ajg33
ORCID:  <http://orcid.org/0000-0002-5711-4872> http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


To arrange a meeting:  <http://doodle.com/ajggray> http://doodle.com/ajggray



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Received on Friday, 7 June 2019 16:38:36 UTC

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