- From: Michel Dumontier <michel.dumontier@gmail.com>
- Date: Fri, 3 Nov 2017 14:29:04 +0100
- To: Leyla Garcia <ljgarcia@ebi.ac.uk>
- Cc: Melanie Courtot <mcourtot@ebi.ac.uk>, public-bioschemas@w3.org
- Message-ID: <CALcEXf50KDBjkYYBGPxmyiySnzouEZXR6_7pxevbp+0=Auvd3g@mail.gmail.com>
yes of course, i was equally surprised to see SIO there in the first place. m. On Fri, Nov 3, 2017 at 1:50 PM, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote: > Hi all, > > IMHO, if we want to be as inclusive as possible, we should not impose > anything outside the scope of type and profile specifications. So, if we > are not to impose RO, SIO, PRO, SO or any other, we should not impose > either OxO. We might find out that other groups also have their own > preferences there (Bioportal mapping, for instance). > > Regards, > > > > On 03/11/2017 11:44, Melanie Courtot wrote: > > 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/BioChemEn > tityAlt-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> > 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 > > > > -- Michel Dumontier Distinguished Professor of Data Science Maastricht University http://dumontierlab.com
Received on Friday, 3 November 2017 13:29:50 UTC