- From: Melanie Courtot <mcourtot@ebi.ac.uk>
- Date: Thu, 2 Nov 2017 10:34:41 +0000
- To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
- Cc: Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
- Message-ID: <f3a9ec7f-33ed-bcf7-5df6-1d8c733525c9@ebi.ac.uk>
Hi Alastair, I'm not sure I understand, are you talking about validating profiles? For validation purpose wouldn't it be equivalent to look for a string such as "isContainedIn" or a URI such as http://purl.obolibrary.org/obo/RO_0001018, where the latter has the advantage to not duplicate existing terms as well as offering dereferencing, hierarchy and flexibility? I'll admit being a bit confused between the 3 examples, so I may be overlooking something. Cheers, Melanie On 02/11/2017 10:18, Gray, Alasdair J G wrote: > Hi Melanie, > > While we are free to pick terms from any ontology, it is important > that as a community we select the terms that we are going to use in > each specific profile. This means that the tooling to use these terms > known what they are looking for. > > Best regards > > Alasdair > >> On 2 Nov 2017, at 10:02, Melanie Courtot <mcourtot@ebi.ac.uk >> <mailto: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" 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 <http://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 <http://schema.org/> >>> >>> -- Justin >>> >>> On Wed, Nov 1, 2017 at 3:56 PM, Gray, Alasdair J G >>> <A.J.G.Gray@hw.ac.uk <mailto: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/ >>> <http://bioschemas.org/specifications/Protein/specification/> >>> BioChemEntity type >>> http://bioschemas.org/specifications/BioChemEntity/specification/ >>> <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/PhysicalEntity/examples/BioChemEntity-min.jsonld >>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntity-min.jsonld> >>> >>> Minimum + Recommended markup using BioChemEntity >>> https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/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/PhysicalEntity/examples/ProteinEntity-min.jsonld >>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/ProteinEntity-min.jsonld> >>> >>> Minimum + Recommended markup using ProteinEntity >>> https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/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/PhysicalEntity/examples/BioChemEntityAlt-min.jsonld >>> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min.jsonld> >>> >>> Minimum + Recommended markup using BioChemEntity and term reuse >>> https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/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 <mailto:A.J.G.Gray@hw.ac.uk> >>> Web: http://www.macs.hw.ac.uk/~ajg33 >>> <http://www.macs.hw.ac.uk/%7Eajg33> >>> ORCID: http://orcid.org/0000-0002-5711-4872 >>> <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. >>> >>> >> > > 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 <mailto:A.J.G.Gray@hw.ac.uk> > Web: http://www.macs.hw.ac.uk/~ajg33 <http://www.macs.hw.ac.uk/%7Eajg33> > ORCID: http://orcid.org/0000-0002-5711-4872 > Office: Earl Mountbatten Building 1.39 > Twitter: @gray_alasdair >
Received on Thursday, 2 November 2017 10:35:08 UTC