- From: Michel Dumontier <michel.dumontier@gmail.com>
- Date: Fri, 3 Nov 2017 10:52:55 +0100
- To: Melanie Courtot <mcourtot@ebi.ac.uk>
- Cc: Justin Clark-Casey <justinccdev@gmail.com>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
- Message-ID: <CALcEXf51KdzCcsQDuZnvzy0CFJ-B7qqV9ciFyDEAB2E4MNP_-w@mail.gmail.com>
SIO is a perfectly acceptable choice, if I say so myself :) m. On Thu, Nov 2, 2017 at 11:02 AM, Melanie Courtot <mcourtot@ebi.ac.uk> wrote: > Hi, > > I'm wondering if we could take it a step further, and instead of defining > specific properties we could just reuse terms from RO (or else)? > > For example, "http://semanticscience.org/resource/is-transcribed-from" > <http://semanticscience.org/resource/is-transcribed-from> could be > replaced by http://purl.obolibrary.org/obo/RO_0002510, "transcribed > from", and "isContainedIn" could be http://purl.obolibrary.org/ > obo/RO_0001018, "contained in". > > Cheers, > Melanie > > -- > Mélanie Courtot, PhD > GA4GH/BioSamples Project lead > European Bioinformatics Institute (EMBL-EBI) > > > > On 01/11/2017 16:18, Justin Clark-Casey wrote: > > Direct term reuse sounds like a good choice to me, especially as > > a) it's the mechanism that schema.org themselves have to add existing > ontology classes and terms to the structured data > b) will make applications much easier to write as they can use existing > general tooling > c) allows us to do everything we were doing with AdditionalProperty and > d) still allows us to define profiles without having to move everything > through schema.org > > -- Justin > > On Wed, Nov 1, 2017 at 3:56 PM, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk> > wrote: > >> Hi All, >> >> Apologies for the delay in sending this email. I have been working with >> Carole on submitting an Implementation Study proposal to the Data Platform >> for more work on Bioschemas. >> >> For representing a specific bioscience type, e.g. a protein, we currently >> have a proposal for using a generic wrapper approach that we then >> specialise, e.g. BioChemEntity specialised with a Protein profile. >> >> Protein profile >> http://bioschemas.org/specifications/Protein/specification/ >> BioChemEntity type >> http://bioschemas.org/specifications/BioChemEntity/specification/ >> >> To help understand the various advantages and disadvantages of this >> approach, Kenneth and I have drawn up an example of marking up a specific >> protein first using the current proposal and second if we were to do the >> same with a specific ProteinEntity. Below are the examples and some >> analysis of them. >> >> *BioChemEntity Example* >> Minimum markup using BioChemEntity >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/BioChemEntity-min.jsonld >> >> Minimum + Recommended markup using BioChemEntity >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/BioChemEntity-min%2Brec.jsonld >> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntity-min+rec.jsonld> >> >> One thing to note is that the minimum + recommended markup is not an >> additive extension of the minimum markup. Due to the use of the >> AdditionalProperty relationship, you need to use an JSON array and add the >> properties from the recommended level within the existing array. >> >> An advantage of this approach is that it reuses terms from existing >> ontologies and we can represent types that do not currently exist in >> Schema.org <http://schema.org>, e.g. Genes, Chemicals, etc. >> >> *ProteinEntity example* >> Minimum markup using ProteinEntity >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/ProteinEntity-min.jsonld >> >> Minimum + Recommended markup using ProteinEntity >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/ProteinEntity-min%2Brec.jsonld >> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/ProteinEntity-min+rec.jsonld> >> >> While the markup in these examples using ProteinEntity is easier to >> interpret, the number of items that need to be changed to markup another >> protein is the same as in the BioChemEntity approach. The simplified markup >> should enable easier adoption, although we could help the current proposal >> of using BioChemEntity by using highlighting on the Bioschemas site to show >> which terms need to be changed. >> >> A major downside of this approach is that we would need to add all the >> types to Schema.org <http://schema.org> or host them at Bioschemas.org >> <http://bioschemas.org>. While these could be mapped to existing terms, >> we would be accused of duplicating existing ontology terms. >> >> *Direct term reuse example* >> Last week, I showed the above examples to Dan (we were at ISWC together). >> He pointed out that the additionalProperty relation was added to allow the >> use of property/value pairs where the properties do not exist in an >> ontology. We are in the situation where the properties we are using come >> from ontologies. Dan suggested that we just use them directly. Note that >> the example also exploits the fact that you can define multiple types. >> >> Minimum markup using BioChemEntity and term reuse >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/BioChemEntityAlt-min.jsonld >> >> Minimum + Recommended markup using BioChemEntity and term reuse >> https://github.com/BioSchemas/specifications/blob/master/Phy >> sicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld >> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld> >> >> As you will see, this seems to have the advantages of both the above >> approaches. The markup is more straightforward than the additionalProperty >> approach, but exploits reusing existing domain ontologies. The tooling and >> exploitation will be much more straightforward. >> >> I invite you all to review and comment on these different examples. Do we >> believe that the BioChemEntity with term reuse (the third set of examples) >> is an appropriate path going forward? >> >> Best regards >> >> Alasdair >> >> PS Sorry for the long email >> >> Alasdair J G Gray >> >> Fellow of the Higher Education Academy >> Assistant Professor in Computer Science, >> School of Mathematical and Computer Sciences >> (Athena SWAN Bronze Award) >> Heriot-Watt University, Edinburgh UK. >> >> Email: 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 >> >> ------------------------------ >> >> *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. Heriot-Watt Services Limited is a private >> limited company registered is Scotland with registered number SC271030 and >> registered office at Research & Enterprise Services Heriot-Watt University, >> Riccarton, Edinburgh, EH14 4AS. >> >> The contents (including any attachments) are confidential. If you are not >> the intended recipient of this e-mail, any disclosure, copying, >> distribution or use of its contents is strictly prohibited, and you should >> please notify the sender immediately and then delete it (including any >> attachments) from your system. >> > > > -- Michel Dumontier Distinguished Professor of Data Science Maastricht University http://dumontierlab.com
Received on Friday, 3 November 2017 09:53:41 UTC