- From: Tony Burdett <tburdett@ebi.ac.uk>
- Date: Wed, 31 Oct 2018 13:37:20 +0000
- To: public-bioschemas@w3.org
Hi Alasdair, all, First - I'm totally supportive of the drive to propose a limited number of entities, I think this is a great idea, it seems highly pragmatic and well aligned with the original vision of the Bioschemas project. But I do have some concerns about the process used to decide which new types should be put forward. What was the rationale for choosing this particular set of entities? Everyone involved in the Bioschemas efforts have spent quite a long period of time collecting detailed usecase and building or designing implementations that deliver on them. This proposal seems to have bypassed some of that work and with a very short time frame for comment. How did you evaluate this set of entities against the existing usecases and current implementations? Speaking for the samples group, I don't think everyone involved has had time to evaluate the impact of this proposal on the samples driving usecases, including the MarRef deployment and Biobanks exchange work. At first reading I think this will make it harder to demonstrate utility for these deployments. If the samples usecases were deprioritized in favour of other more compelling examples, that's reasonable, but the proposal document doesn't indicate how this was determined and I'd like to have a chance to review the results of that decision-making process. Thanks, Tony On 31/10/2018 10:01, Gray, Alasdair J G wrote: > Hi All, > > This is a reminder that you have until the end of tomorrow to comment > on the proposed changes to Bioschemas that are presented in the > document at the following link. > https://docs.google.com/document/d/1Cw9K25N1l-Lbet1cahJuFtYgNKiF76apGcCqJPSeuZg/edit?usp=sharing > > Best regards > > Alasdair > >> On 26 Oct 2018, at 15:51, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk >> <mailto:A.J.G.Gray@hw.ac.uk>> wrote: >> >> Thanks to those who have already reviewed and commented on the document. >> >> I have added an addendum to the document which includes the proposal >> for the DataRecord type. Sorry for the omission of this in the >> original version of the document. >> >> Best regards >> >> Alasdair >> >>> On 25 Oct 2018, at 16:27, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk >>> <mailto:A.J.G.Gray@hw.ac.uk>> wrote: >>> >>> Dear Bioschemas Community >>> >>> It has been a little over a year since we had the last community >>> face-to-face, during which time we have achieved a lot, with 44 >>> resources publishing markup on over 6 million web pages [1]. Just >>> over a month ago we also saw the launch of Google's Dataset Search >>> [2] through which we should see some of the promised benefit from >>> the Bioschemas markup. >>> >>> In the last few weeks, there have been several active discussions on >>> github issues (210, 215, 217, 218, 220, 221, 222, 223) [3] relating >>> to the extension of schema.org <http://schema.org/> types and >>> properties for life sciences. Bioschemas is intended as a simple >>> markup mechanism that should be easy to implement for providers and >>> consume by tools. In practice we have made things hard. >>> >>> Based upon our experiences, including those from running several >>> tutorials with groups outside of Bioschemas “family”, we have >>> identified two main problems with our current community approach of >>> using existing life sciences ontology classes. >>> >>> * >>> >>> The first problem is that generic consumers of the markup, e.g. >>> search engines such as Google, will not understand the life >>> sciences ontology classes; these services only understand types >>> and properties in the schema.org <http://schema.org/> vocabulary >>> and this will not change. Consequently, under the current >>> approach, these generic services will not be able to distinguish >>> between a BioChemEntity that is a Protein or a Gene, they will >>> just understand them all as BioChemEntity. Thus there will be no >>> benefit to the resources (eg. individual databases) in these >>> services (Google) consuming the markup. >>> >>> * >>> The second is that the choice of classes and terms from specific >>> life sciences ontologies are not compatible with the nature of >>> the schema.org <http://schema.org/> vocabulary. This leads to >>> logical inconsistencies for services that consume the markup. >>> >>> To overcome these challenges, we propose that a limited number of >>> new types and properties should be added to schema.org >>> <http://schema.org/> as hosted extensions. These have been developed >>> in discussion with Dan Brickley (chair of the schema.org >>> <http://schema.org/> community group) and will serve as bridging >>> terms between the generic schema.org <http://schema.org/> vocabulary >>> and the more specific life sciences ontologies. We anticipate that >>> there will be further types proposed in the future, e.g. chemical. >>> >>> The proposal is available in the following google document. Only >>> comment permissions have been granted so that the original proposal >>> is unchanged. >>> >>> https://docs.google.com/document/d/1Cw9K25N1l-Lbet1cahJuFtYgNKiF76apGcCqJPSeuZg/edit?usp=sharing >>> >>> In order that these changes can be in place by the biohackathon we >>> request any comments on these proposals are made by 1 November. >>> >>> Best regards >>> >>> Alasdair, Leyla, Sarala, Nick, Carole, and Rafa >>> >>> [1] http://bioschemas.org/liveDeploys/ >>> >>> [2] https://toolbox.google.com/datasetsearch >>> >>> [3] https://github.com/BioSchemas/specifications/issues/ >>> -- >>> 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 <mailto: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. >>> >> >> -- >> 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 <mailto: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 > > -- > 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 <mailto: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 > -- Tony Burdett Technical Co-ordinator - Samples, Phenotypes and Ontologies Team, European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: + 44 (0) 1223 494 624
Received on Wednesday, 31 October 2018 13:38:27 UTC