W3C home > Mailing lists > Public > public-bioschemas@w3.org > November 2017

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

From: ljgarcia <ljgarcia@ebi.ac.uk>
Date: Fri, 17 Nov 2017 13:06:15 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: Melanie Courtot <mcourtot@ebi.ac.uk>, public-bioschemas@w3.org
Message-ID: <9f9194cc255da84648514c21283c48d8@ebi.ac.uk>
Hi all,

Regarding Alasdair proposed voting: +1

Now, in order to address Melanie's (and possible others') concerns, I 
propose a second separated voting on the terms to be used.

As Alasdair has explained, if his proposal (yes or not to use fixed 
agreed third-party terms for profile types and properties) is accepted, 
then all profiles will provide a set of terms for the type and 
properties (minimum, recommended, optional). The profile groups will 
share with everybody their proposal, with some explanation on their 
selected terms as part of the description (maybe term usage within the 
community, clarity of definition, etc.). Then, anyone could raise their 
hand and vote yes or propose an alternative. A valid alternative could 
be for instance to move something from minimum to recommended or to 
change the chosen term together with some justification. Depending on 
the proposed alternatives, we might need a video conference to get to an 
agreement on profile basis.

I would also suggest to focus on Alasdair proposal to start with. More 
agreements will come later.


On 2017-11-17 10:44, Gray, Alasdair J G wrote:
> Hi All,
> I have started a new thread so that we can have a clear starting point
> for the state of the current discussion. We are now at a stage where
> we need to make a decision, and I propose that we try to have
> consensus by midnight Hawaii time on Thursday 23 November*.
>  	* We have agreed that where a suitable schema.org [1] term does not
> exist we will use an suitable existing ontology term directly rather
> than through the additionalProperty mechanism.
> 	* The consensus is now for a profile to state a suitable ontology
> term.
>  	* A future revision of the profile will be free to replace that
> ontology term with another term if there is community consensus for
> such a change.
> 	* Data providers will also be free to provide additional terms with
> the same meaning.
> 	* To support the development of common markup, a json-ld context will
> be provided on the bioschemas site.
>  	* We will look into the feasibility of versioning this so that when
> a specification is updated the context will reflect those changes.
> If you agree with the above, simply reply with a +1. Otherwise please
> provide a counter proposal or amendment.

On 2017-11-17 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 [1].
>> 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 [2]
>> 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
> Links:
> ------
> [1] http://schema.org/
> [2] http://www.macs.hw.ac.uk/%7Eajg33
Received on Friday, 17 November 2017 13:06:39 UTC

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