- From: Chris Mungall <cjmungall@lbl.gov>
- Date: Mon, 13 May 2019 07:51:14 -0700
- To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
- Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
- Message-ID: <CAN9AifspsUPG_P8dV9VtyNhETX9Pr6Fp+ABq2GYnh5C9npDfMg@mail.gmail.com>
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 > > ------------------------------ > > *Heriot-Watt University is The Times & The Sunday Times International > University of the Year 2018* > > Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With > campuses and students across the entire globe we span the world, delivering > innovation and educational excellence in business, engineering, design and > the physical, social and life sciences. This email is generated from the > Heriot-Watt University Group, which includes: > > 1. Heriot-Watt University, a Scottish charity registered under number > SC000278 > 2. Edinburgh Business School a Charity Registered in Scotland, > SC026900. Edinburgh Business School is a company limited by guarantee, > registered in Scotland with registered number SC173556 and registered > office at Heriot-Watt University Finance Office, Riccarton, Currie, > Midlothian, EH14 4AS > 3. Heriot- Watt Services Limited (Oriam), Scotland's national > performance centre for sport. 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Received on Monday, 13 May 2019 14:52:03 UTC