Re: Proposal refinement

Chris,

This is being in done in the context of schema.org<http://schema.org> where it is intended to be a looser semantics that enable search.

These mappings will not be included in the submission to schema.org<http://schema.org>, but would be maintained separately by bioschemas.

Alasdair

On 2 Nov 2018, at 16:13, Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>> wrote:


Do we need more information before casting a vote on #227?

The property to be used depends on the use cases for bioschemas. If bioschemas is to be treated as an ontology and used within any kind of logical inference context, then RDFS/OWL properties are indeed stronger, but this means they should also be used with care. If you subProperty an ObjectProperty, and then try and use this with a text value rather than an object, then you get into trouble. Similarly if you subPropertyOf off of a SIO or OBO property, and it has domain and range constraints that don't fit with looser usage in bioschemas. This is even more true for the stronger equivalentProperties axiom. I would be very wary of adding logical axioms in an ad-hoc fashion, without having a workflow where you use an OWL reasoner to validate what you are saying for consistency and coherency.

If instead bioschemas is just intended as a loose guide for adding minimal structure for web pages maximising chances of being indexed by google, then the logical properties don't really matter. You should just choose whatever has the maximal chance of google doing something useful with.

Either way, you connection between the bioschemas property and the ontology property should be clearly documented for human users.

Apologies if I'm alone in missing some of the bigger picture here.

On 2 Nov 2018, at 8:37, Gray, Alasdair J G wrote:

Dear Bioschemas Community,

Thank you to everyone who has taken part in the review of the proposed changes to Bioschemas. In general there has been broad agreement to the idea of introducing 5 new types to schema.org<http://schema.org/>. There are however still a few issues to resolve. To enable this, I have created a cleaned up version of the proposal. The previous version is still available with all the comments on it as a record of the discussion.

The cleaned up proposal can be found at the following link. Again, only comment access has been provided.
https://docs.google.com/document/d/1FCLcjlsC_xfUCwKy-HnwockRexVcMUHAAGohfTryh08/edit?usp=sharing


We need to reach a decision on the following cross-cutting questions. I have created GitHub issues to allow a vote to be taken on these.

Should BioChemEntity inherit from Intangible?
Please use the following issue to cast your vote.
https://github.com/BioSchemas/specifications/issues/226


Should we use rdfs:subPropertyOf to link to ontology terms?
Please use the following issue to cast your vote.
https://github.com/BioSchemas/specifications/issues/227


Finalising Properties

There are two properties that are still causing issues and the discussion in the previous document was not conclusive.

contains: we still need to understand what this relationship is being used for. I have attempted to refocus the discussion.

position: I have left the discussion in place for this property. However, I wonder if ‘positionInRepresentation’ would more accurately capture the desired usage.


As before, we are trying to wrap things up ahead of the Biohackathon. Please can I ask that we have these issues resolved by the end of Monday (I know this is not much time).

Best regards

Alasdair

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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

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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
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