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Re: Google Summer of Code

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Mon, 22 Jan 2018 10:10:37 +0000
To: "Rafael C. Jimenez" <rafael.jimenez@elixir-europe.org>
Cc: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, public-bioschemas@w3.org, squizzat@ebi.ac.uk, Nicola Buso <nbuso@ebi.ac.uk>, Rodrigo Lopez <rls@ebi.ac.uk>, Federico López <fico89@gmail.com>, Alexander Garcia Castro <alexgarciac@gmail.com>, "oxgiraldo@gmail.com" <oxgiraldo@gmail.com>
Message-ID: <376bc9fc-b464-3589-691b-ff846161a34b@ebi.ac.uk>
Hi all,

I liked Federico's idea and I could collaborate with it so I have added 
my name as a second mentor.

Alexander, who recently subscribed to the mailing list, added a new 
project regarding a mapping between JATS and schema.org. The basic idea 
would be to follow the Bioschemas model (cardinality/marginality) so 
other groups can use it for citations. Furthermore, a parser from JATS 
to Bioschemas would be developed. This would be amazing for 
publications. Olga and I will help as secondary mentors for that project.

I mentioned the idea about the EBI-search but we have not heard from 
Rodrigo so I did not included in the GSoC document. We could add it 
later if we see it is feasible.


On 19/01/2018 09:34, Rafael C. Jimenez wrote:
> Hi Leyla,
> Sorry for the late reply.
> Related to the EBI search. I imagine you mean the EBI search summary 
> pages? Something like this would require the involvement of Rodrigo's 
> team at the EBI (CCed). I remember in one of Bioschemas workshops we 
> briefly discussed this as an application. I don't remember who, but I 
> think Rodrigo, Silvano or Nicola suggested the EBI search summary 
> pages could use Bioschemas as input. Below 3 ideas I thought could be 
> interesting to be explored by a student related to this topic. It 
> would be great to count on Rodrigo, Nicola and Silvano if they are 
> interested.
>  1. Demonstrate how the EBI summary results
>     <https://www.ebi.ac.uk/s4/summary/molecular?term=VAV_HUMAN&classification=9606&tid=protOrthVAVHUMAN>
>     (gene, expression, protein, protein structure and literature)
>     could be built consuming Bioschemas from the original data
>     sources. In my opinion this would require A.- demonstrating how
>     the contributing EBI resources (Ensembl, Expression atlas,
>     Uniprot, ...) can expose the necessary information with Bioschemas
>     and B.- demonstrate how to render the summary results as they are
>     presented by the EBI search consuming Bioschemas.
>  2. Demonstrate how the EBI search result pages could be marked up
>     with Bioschemas
>  3. Explore and propose a strategy to integrate 3rd party summary data
>     via Bioschemas (similar to the idea of Track Hubs and DAS but with
>     Bioschemas)
> Regards,
> Rafa
> On 15 Jan 2018 10:51, "Leyla Garcia" <ljgarcia@ebi.ac.uk 
> <mailto:ljgarcia@ebi.ac.uk>> wrote:
>     Hi Alasdair,
>     I like the Validata project, let me know if I can collaborate
>     somehow with it.
>     The EBI search could be done as well using Bioschemas markup so
>     that would be a possibility as well. I could help redacting the
>     idea behind but I am afraid not this week. @Rafael, what do you
>     think of this idea? This is something you have mentioned in the past.
>     Cheers,
>     On 11/01/2018 15:54, Gray, Alasdair J G wrote:
>>     Hi All,
>>     We would like to propose Bioschemas as a Google Summer of Code
>>     organisation (deadline 23 January 2018).
>>     https://summerofcode.withgoogle.com/
>>     <https://summerofcode.withgoogle.com/>
>>     I have started drafting ideas for projects in a google document,
>>     please feel free to add more project ideas or details to my
>>     initial brain dump.
>>     https://docs.google.com/document/d/1_i2vqUfCy1laVbslVR6kjaRLIUN8Y2nqQIEPT8G68gg/edit
>>     <https://docs.google.com/document/d/1_i2vqUfCy1laVbslVR6kjaRLIUN8Y2nqQIEPT8G68gg/edit>
>>     Best regards
>>     Alasdair, Carole, and Rafa
>>     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 <mailto:A.J.G.Gray@hw.ac.uk>
>>     Web: http://www.macs.hw.ac.uk/~ajg33
>>     <http://www.macs.hw.ac.uk/%7Eajg33>
>>     ORCID: http://orcid.org/0000-0002-5711-4872
>>     <http://orcid.org/0000-0002-5711-4872>
>>     Office: Earl Mountbatten Building 1.39
>>     Twitter: @gray_alasdair
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Received on Monday, 22 January 2018 10:11:05 UTC

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