- From: Melanie Courtot <mcourtot@ebi.ac.uk>
- Date: Fri, 3 Nov 2017 11:44:45 +0000
- To: public-bioschemas@w3.org
- Message-ID: <1ed19606-6f8a-ad6e-b9b7-1e2a07db5402@ebi.ac.uk>
Hi Michel, By "a step further" I was trying to make 2 points (and looking back my email was probably not explicit enough): - Bioschemas should probably steer clear of debating the best choice of ontology. In general, and as I mentioned during the last meeting, we probably don't want to constrain which resources are being used as different communities/users/groups will have their favorite ones, and will probably not want to recode. Leyla mentions exisiting mappings, and we could rely on the OxO tool [1] as well. It'd be interesting to see if we could make this work with validation tools. - I don't think we should declare many Bioschemas specific properties provided there is a mechanism for reusing existing relations. In the current example at https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min.jsonld <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min.jsonld> there is a "isContainedin" which I don't think Bioschemas should redefine for example (and I see both SIO and RO have the relation already) Cheers, Melanie [1] https://www.ebi.ac.uk/spot/oxo/index On 03/11/2017 09:52, Michel Dumontier wrote: > 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 > <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" > <http://semanticscience.org/resource/is-transcribed-from> could be > replaced by http://purl.obolibrary.org/obo/RO_0002510 > <http://purl.obolibrary.org/obo/RO_0002510>, "transcribed from", > and "isContainedIn" could be > http://purl.obolibrary.org/obo/RO_0001018 > <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. >> >> > > > > > -- > Michel Dumontier > Distinguished Professor of Data Science > Maastricht University > http://dumontierlab.com
Received on Friday, 3 November 2017 11:45:12 UTC