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Re: Dissemination of Bioschemas specifications

From: ljgarcia <ljgarcia@ebi.ac.uk>
Date: Thu, 27 Jul 2017 09:39:57 +0100
To: Tony Burdett <tburdett@ebi.ac.uk>
Cc: Michel Dumontier <michel.dumontier@gmail.com>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, Carole Goble <carole.goble@manchester.ac.uk>, public-bioschemas@w3.org
Message-ID: <cd3fd3fd1dee66fe402f21c40794a1e3@imap.ebi.ac.uk>
Hi Tony,

It is great having someone from the samples side! Welcome on board!

Please feel free to add any comments or suggestions. Please bear in mind 
that we will not actively work on the specification right now but in 
September during the hackathon. So you will not see much changes now but 
more like discussion and so. I will of course keep an eye on the 
document so will take a look to your comments and suggestions and will 
require additional information if needed. We can also meet at EBI any 
time and have a look together.

We want to end up with a lightweight specification with just a bunch of 
properties, that can fit as many biological entities as we can think of. 
If samples require something more specific, we can always move it to its 
own type, ideally extending from Biological Entity.

Regards,


On 2017-07-26 14:56, Tony Burdett wrote:
> Thanks Leyla,
> 
> I’d like to be involved in finalising the specification.  I have
> some comments from the samples side and some usecases that I don’t
> think the current specification fully supports.  If I have additions
> to make to the spec how would you like me to propose them, via
> comments in the specification document or with suggestions?
> 
> Thanks,
> 
> Tony
> 
> --
> Tony Burdett
> Technical Co-ordinator - Samples, Phenotypes and Ontologies Team,
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: + 44 (0) 1223 49 4624
> 
>> On 26 Jul 2017, at 11:26, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:
>> 
>> Hi all,
>> 
>> We had some comments/discussion going on on the spredasheet that
>> have now been moved to the specification document. If you want to
>> participate, please use the specification document
>> 
> (https://docs.google.com/document/d/1XASuESIHU3bi1aXMxQS5-rCOQX0ugjMNkh68VF4co4Q)
>> 
>> I will meet with Michel during the second week of September to
>> finalize the specification for the Biological Entity. If you want to
>> participate in the discussion, please let us know so we can set up
>> the right channel.
>> 
>> Regards,
>> 
>> On 26/07/2017 10:34, Michel Dumontier wrote:
>> 
>> great thanks
>> i've added comments to the spec
>> 
> https://docs.google.com/document/d/1XASuESIHU3bi1aXMxQS5-rCOQX0ugjMNkh68VF4co4Q/edit?ts=59785c55#
>> 
>> will discuss with Leyla and. I'll see Leyla at the biohackathon in
>> Sept, and am planning to come to the october bioschemas meeting
>> 
>> m.
>> 
>> On Wed, Jul 26, 2017 at 9:21 AM, Gray, Alasdair J G
>> <A.J.G.Gray@hw.ac.uk> wrote:
>> 
>> You can find links to the specs and also the github tracker for each
>> group on the bioschemas website.
>> 
>> http://bioschemas.org/groups/
>> 
>> 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 [1]
>> 
>> -------------------------
>> 
>> FROM: Carole Goble <carole.goble@manchester.ac.uk>
>> SENT: Tuesday, July 25, 2017 9:09:15 PM
>> TO: Michel Dumontier
>> CC: Gray, Alasdair J G; public-bioschemas@w3.org
>> SUBJECT: Re: Dissemination of Bioschemas specifications
>> 
>> 1. I stand corrected - Norman had some lovely slides on the marine
>> use case
>> 2. Michel - the specs are still in the googledocs so you can comment
>> right there
>> 
>> Carole
>> 
>> Hi all,
>> I had a chance to chat with Leyla at her poster today. I shared
>> with her some feedback. Just wondering if there is a particular
>> communications channel i should use for written feedback?
>> 
>> m.
>> 
>> On Tue, Jul 25, 2017 at 9:02 PM, Carole Goble
>> <carole.goble@manchester.ac.uk> wrote:
>> 
>> They are my slides mainly - it was the spoken narrative
>> Carole
>> 
>> Sent from my iPhone by
>> Professor Carole Goble
>> The University of Manchester
>> UK
>> 
>> On 25 Jul 2017, at 15:32, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
>> wrote:
>> 
>> Are Norman’s slides available?
>> 
>> Alasdair
>> 
>> On 25 Jul 2017, at 14:46, Carole Goble
>> <carole.goble@manchester.ac.uk> wrote:
>> 
>> The bioschemas talk and poster at BOSC also attracted a great deal
>> of interest as did the bioschema part in elixir interoperability
>> talk in the elixir session at ismb. Norman did a really great job of
>> putting the reasons and benefits in terms that were immediately
>> understandable and not about the technology but the benefit.
>> 
>> I'm giving a keynote at SWAT4LS - I'm going to be talking about
>> elixir work - notably CWL, research objects and bioschemas.
>> 
>> Carole
>> 
>> Sent from my iPhone by
>> Professor Carole Goble
>> The University of Manchester
>> UK
>> 
>> On 25 Jul 2017, at 15:31, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
>> wrote:
>> 
>> Hi Leyla,
>> 
>> Thanks for all your efforts in publicising the Bioschemas work. I
>> hope that your poster presentation went well at ISMB.
>> 
>> I agree that we should consider putting something together for
>> SWAT4LS. We also need to consider what other publications we are
>> aiming to write about this work.
>> 
>> Best regards,
>> 
>> Alasdair
>> 
>> On 27 Jun 2017, at 09:43, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:
>> 
>> Hi all,
>> 
>> We will have a poster at Bio-ontologies (ISMB) this year. It was
>> meant to be about the protein case but now that we have
>> BiologicalEntity as an umbrella it will probably cover much more
>> than just proteins. ISMB is scheduled for the 4th weekend of July so
>> I will share with you all the poster a couple of weeks before that.
>> I hope we will gather some feedback about our proposal.
>> 
>> We will also participate in the Biohackathon this year, second week
>> of September. As it happens right before our next meeting, I plan to
>> go ahead with some of the implementation work. In particular, I will
>> work on a javascript module to gather protein related information. I
>> will do my best to make it as generic as possible so it can be
>> modified in order to work for other entities. If by that time there
>> is already a validation tool or any other supporting Bioschemas
>> specifications, it would be wonderful to get some more information
>> before hands.
>> 
>> And, SWAT4HCLS call for papers has been recently announced
>> (http://swat4ls.blogspot.co.uk/2017/06/swat4ls-2017-cfp-is-out.html
>> [2]). We should submit either a poster or a paper there as well.
>> Deadline for paper abstract is 22.Sep with full submission on
>> 06.Oct.
>> 
>> Regards,
>> 
>> 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 [3]
>> ORCID: http://orcid.org/0000-0002-5711-4872 [4]
>> Office: Earl Mountbatten Building 1.39
>> Twitter: @gray_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 [3]
> ORCID: http://orcid.org/0000-0002-5711-4872 [4]
> Office: Earl Mountbatten Building 1.39
> Twitter: @gray_alasdair
> 
>  --
> 
> Michel Dumontier
> Distinguished Professor of Data Science
> Maastricht University
> http://dumontierlab.com [7]
> 
> --
> Professor Carole Goble CBE FREng FBCS CITP
> School of Computer Science
> University of Manchester
> Manchester, UK
> 
> tel: +44 161 275 6195 [5]
> email: carole.goble@manchester.ac.uk
> twitter: @CaroleAnneGoble
> 
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> 
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>  --
> 
> Michel Dumontier
> Distinguished Professor of Data Science
> Maastricht University
> http://dumontierlab.com [7]
> 
> 
> 
> Links:
> ------
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> [2] http://swat4ls.blogspot.co.uk/2017/06/swat4ls-2017-cfp-is-out.html
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Received on Thursday, 27 July 2017 08:40:23 UTC

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