Re: Vote on usage of non-schema.org terms

On Fri, Nov 17, 2017 at 1:13 PM, Philippe <proccaserra@gmail.com> wrote:

> Hi Alisdair,
>
> Based on the questions asked by Melanie and Andra, it seems there are 2
> issues:
>
> 1. Are there preferred resources from which terms should be drown?
>     If so, the Bioschema group should list those resources and declare the
> criteria for selection/inclusion.
>
> 2. Is it OK for developers to disregard these bioschema-vetted resources
> and provide an bioschema json instantiation but typed in their preferred
> semantic frameworks
>
> I agree with Michel that ideally, the group should converge to a common
> framework to increase interoperability but this proove painful
>
> Andra's suggestion alleviates that issue at the expense of creating
> mapping needs, but this could be asked from the implementers to provide the
> mapping if they decide to stray away from the bioschema preferred ways.
>

>From an application point of view, I think that a mapping isn't a huge
burden as long as it's provided by bioschemas and is easily machine
consumable.  It's when these are being generated after the fact (by machine
learning, etc.) that things start getting complicated.

If there is a bioschemas mapping then perhaps any agreed URL for a
particular concept can be used in the JSON-LD, if providers cannot use the
preferred or canoncial one.


> Philippe
>
>
>
>
> On 17/11/2017 12:35, Gray, Alasdair J G wrote:
>
> Hi Melanie, All,
>
> For clarification, the vote is for when a profile makes a statement that
> it needs a term (either minimal, recommended, or optional) for a specific
> property, then it makes a declaration about the ontology term that is to be
> used.
>
> I used Protein as an example, it would be up to the Protein profile
> developers to discuss and agree on the term.
>
> Alasdair
>
>
> On 17 Nov 2017, at 12:05, Melanie Courtot <mcourtot@ebi.ac.uk> wrote:
>
> Alasdair, all,
>
> The ask was for a vote or counter proposal/amendment; I provided the
> latter.
>
> You mention that the Protein working group has agreed that they require
> addition of an additional property. I don't think it is fair to ask all
> working groups to agree on a solution without giving them a chance to raise
> alternatives. If this vote is *only* for the Protein working group property
> then this group only should vote; but I thought we were here making a
> critical design decision for all of Bioschemas.
>
> You have previously stated that you believed we should fix terms to a
> particular ontology URI, I am here stating that I am not fundamentally
> disagreeing but that I would like this to be limited to profile types.
> Specifically in this case my vote would be no about fixing the property
> which connects to the gene (and others have raised issues with this
> property).
>
> I therefore propose that either this vote is amended to make it clear that
> we are voting on *only* the connection to gene for the Protein working
> profile or an additional option be added to the vote in which we consider
> the option of fixing the URIs but *only* for the profile types. I would
> also add that choosing the latter allows us to move forward as a group
> right now, and doesn't precludes us from revisiting this issue once we have
> started deploying markups and have more practical experience with what
> works well and what doesn't. It may very well be that we then realize we
> should constrain further, but IMO this decision would be premature at this
> stage.
>
> Cheers,
> Melanie
>
>
>
>
>
>
> On 17/11/2017 11:43, Gray, Alasdair J G wrote:
>
> Hi
>
> On 17 Nov 2017, at 11:00, Melanie Courtot <mcourtot@ebi.ac.uk> wrote:
>
> I would like to offer an alternative, as stated by Andra: "Wouldn't the
> best option simply be to be strict on the type Protein, but for the
> remaining properties use the complete ontological space out there, without
> any limitations.", where the type Protein would be replaced by others as
> appropriate.
>
>
> I don’t see that this helps us with the search use case that has been
> identified by the Protein working group which has agreed that having the
> connection with gene is a minimal property. As such, in the bioschemas
> approach a property needs to be used for the connection to gene.
>
> The purpose of this vote is then to see whether we use profiles to fix
> that term to a particular ontology URI, as there is not a suitable term in
>  schema.org.
>
> By leaving things totally unconstrained, data providers must select a term
> to use and then hope that the clients can interpret the selected term.
>
> The Bioschemas approach is about specifying the terms to use. Thus I
> believe that we should state the ontology term to use. This makes both
> adoption of markup easier (no choices to be made) and the use of the markup
> (the tool knows what to expect and how to interpret the terms).
>
> Alasdair
>
> 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
>
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> 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
>
>
>