W3C home > Mailing lists > Public > public-bioschemas@w3.org > January 2018

Re: Google Summer of Code

From: Rafael C. Jimenez <rafael.jimenez@elixir-europe.org>
Date: Mon, 22 Jan 2018 11:43:23 +0000
Message-ID: <CABH4q18EvY5DwJ61dAA_HYW3afEmhSR9Uq6RcW9GyhoT3+_Bhg@mail.gmail.com>
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
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>
Jut a kind reminder we will be making the application tomorrow. Today at
14:00 GMT I will take the content of the google doc to create a GSoC web
page in the Bioschemas website. So if you have anything else to add please
try to do it within the next 2 hours.

Regards,
Rafa

On 22 January 2018 at 10:10, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:

> 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.
>
> Regards,
>
>
> 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> 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/
>
> 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_i2vqUfCy1laVbslVR6kjaRL
> IUN8Y2nqQIEPT8G68gg/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
> 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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-- 

*Rafael C Jimenez*
ELIXIR Chief Technical Officer
www.elixir-europe.org

ELIXIR Hub, South Building
Wellcome Genome Campus
Hinxton, Cambridge, CB10 1SD, UK
Tel: +44 (0) 1223 49 2574 <%2B44%20%280%29%201223%20492574>
E-Mail: rafael.jimenez@elixir-europe.org [image: ELIXIR]
<http://www.elixir-europe.org/>
Received on Monday, 22 January 2018 11:44:10 UTC

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