Re: What to do at the Biohackathon Re: [Urgent] Proposed changes to Bioschemas

Dear Jerven

Thanks for your involvement in the discussions over the course of the last week. Your input is very much appreciated. However, I do not believe that we are as far away as you make out. The proposals put forward are based on the outcomes of the last couple of years activity. The main difference being these are being proposed as types that will be proposed for schema.org rather than just being usage conventions that draw on terms from existing vocabularies. I have made a cleaned up version of the proposal that I have shared in a separate email thread.

With regards to the biohackathon, we will go ahead with developing markup with the core data resources present and using the experience to further refine and improve bioschemas. We will start with the generic types like Dataset but aim to get down to the level of genes and proteins. We cannot keep delaying forever waiting for the perfect proposal. Bioschemas had always been about prototyping and then refining based on practical experience.

The key thing for the Biohackathon will be to get some form of markup deployed. It is far easier to make minor tweaks and refinements than it is to make the initial deployment. In all that we are suggesting, the deployment mechanism does not change.

Best regards

Alasdair

http://www.macs.hw.ac.uk/~ajg33

________________________________
From: Jerven Bolleman <jerven.bolleman@sib.swiss>
Sent: Friday, November 2, 2018 1:51:40 PM
To: public-bioschemas@w3.org
Subject: What to do at the Biohackathon Re: [Urgent] Proposed changes to Bioschemas

Dear Bioschemas Community,

In approximate one week, on November 12th, the Biohackathon in Paris
will start. The latest proposal has raised very long comment threads,
and key discussions had to be moved from the google doc into e-mail
lists. The proposal contains necessary but drastic changes from drafts
0.3-0.5 for the Protein part, that have not been tested yet.

I believe we did not have enough time to finalize the discussions and
think about all consequences by the deadline of yesterday. We still
don't know if we will have a Datarecord or not and how things are going
to be placed in the schema.org hierarchy.

Most Core Data Resources cannot afford to invest efforts in unfunded
projects, we must therefore try to keep their investments low. If we ask
them now to implement this proposal, we cannot ask them in a few months
to change the implementation again.

This leaves the question of what should be done at the Biohackathon:

- Should we ask people to implement first pure schema.org (e.g.
DataCatalog, DataSet, Action etc...) and not yet any of the bioschema
gene,protein ones?

- Should we take the opportunity to present the proposal and its open
questions to gather feedback and make a reality check?


Regards.
Jerven

On 10/25/2018 05:27 PM, Gray, Alasdair J G 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
>
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