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Re: Very rough prototype implementation of DataCatalog/Dataset schema.org markup in InterMine

From: Justin Clark-Casey <justinccdev@gmail.com>
Date: Wed, 24 May 2017 09:55:53 +0100
Message-ID: <CAME9NR_7S+9pnOB+decyCQOOubrVkVxiPo0DEDCPv2oxfjf_WQ@mail.gmail.com>
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>, "Rafael C. Jimenez" <rafael.jimenez@elixir-europe.org>
Sure, I'd be happy to.

On 24 May 2017 at 09:33, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk> wrote:

> Hi Justin
> Thanks for doing this and pushing forward everyone's understanding.
> I know this is really short notice but could you present the highlights of
> your work this afternoon?
> Alasdair J G Gray
> Fellow of the Higher Education Academy
> Assistant Professor in Computer Science
> Herriot-Watt University, Edinburgh
> www.macs.hw.ac.uk/~ajg33 <http://%3Cbr/%3Ewww.macs.hw.ac.uk/~ajg33>
> ------------------------------
> *From:* Justin Clark-Casey <jc955@cam.ac.uk>
> *Sent:* Tuesday, May 16, 2017 3:54:15 PM
> *To:* public-bioschemas@w3.org
> *Subject:* Very rough prototype implementation of DataCatalog/Dataset
> schema.org markup in InterMine
> Hi all.  In advance of the Bioschemas meeting next week, I've hacked up a
> very rough implementation of schema.org markup in InterMine [1].
> Specifically, this
> is in an installation of InterMine called Synbiomine [2], a data warehouse
> for synthetic biology that I've been working on.  This compiles information
> from many
> sources (EBI, NCBI, etc.) into integrated biological object reports
> (genes, proteins, parts, etc.).
> In lieu of of 'proper' Bioschemas structures, I've put in DataCatalog and
> Dataset.  In fact, I'm abusing Dataset to represent integrated objects
> (e.g. protein
> Q816S6_BACCR) but I wanted to experiment with linking structures (in this
> case DataCatalog and Dataset).  The front page embeds the DataCatalog and
> individual
> report pages (e.g. [3]) embed Dataset.  You can see the Google Structured
> Data Testing Tool (GSDTT) analysis of the front page at [4] and a
> particular report
> pages at [5].
> My top 5 immediate observations:
> * Embedding JSON-LD itself is not hard.  More challenging is interpreting
> which schema.org properties to use and how to use them (e.g.
> CreativeWork.about or
> Thing.description)?
> * Being able to link DataCatalog and Dataset (via dataset and
> includedInDataCatalog attributes) feels like a big win to embed
> standardized structure in a
> website.  In my case, however, I have 2m+ 'datasets' and this may cause
> issues embedding in a single DataCatalog structure (in my implementation
> I've
> artificially limited this to 500).  This may be due to my abuse of Dataset
> but the same problem could crop up in other contexts.
> * Also in linking DataCatalog and Dataset, I am just embedding the Dataset
> url in the DataCatalog, for instance, and assuming software will navigate
> to the
> Dataset and extract more information from that page.
> * The GSDTT is essential for checking the markup and having some
> implementation for Bioschemas specifications will be very useful.
> * The GSDTT for some reason does not show multiple entries for the same
> property (e.g. shows only one citation in [5] even though there are many).
> I presume
> this is just a GSDTT limitation.
> Overall, imo, it feels really nice to embed structured bio information
> directly in the website and this could be really valuable if all the markup
> is
> consistent.  Tooling here like GSDTT may be a big help.
> [1] http://intermine.org/
> [2] http://beta.synbiomine.org/synbiomine/begin.do
> [3] http://beta.synbiomine.org/synbiomine/report.do?id=112968868
> [4] https://search.google.com/structured-data/testing-tool#
> url=http%3A%2F%2Fbeta.synbiomine.org%2Fsynbiomine%2Fbegin.do
> [5] https://search.google.com/structured-data/testing-tool#
> url=http%3A%2F%2Fbeta.synbiomine.org%2Fsynbiomine%
> 2Freport.do%3Fid%3D112968868
> Regards,
> --
> Justin Clark-Casey, Synbiomine/InterMine Developer
> http://synbiomine.org
> http://twitter.com/justincc
> ------------------------------
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Received on Wednesday, 24 May 2017 08:57:46 UTC

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