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Re: Blue Brain Nexus - A knowledge graph for data-driven science https://bbp-nexus.epfl.ch/staging/docs/

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Mon, 15 Jan 2018 11:20:56 +0000
To: Carole Goble <carole.goble@manchester.ac.uk>, Andra Waagmeester <andra@micelio.be>, Philippe <proccaserra@gmail.com>
Cc: Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>, Sy Mohameth François <mohameth.sy@epfl.ch>, Justin Clark-Casey <justinccdev@gmail.com>, BATISTA Dominique <Dominique.BATISTA@france-bioinformatique.fr>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Paolo Missier <paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>, "pinarpink@yahoo.com" <pinarpink@yahoo.com>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>
Message-ID: <65b3ca90-2a8d-868a-4cc6-f4d55d45f608@ebi.ac.uk>
Hi Carole,

Sorry about my late response. Could you please invite me to join the 
group? If you are still looking for volunteers to lead the group, I 
could help (maybe). Just please give me some more days to go through the 
emails and see how I could contribute. I am still away this week so do 
not expect to catch up before next week.

Regards,

On 04/01/2018 13:44, Carole Goble wrote:
>
>
>
> Andra
> I started up a bioschemas team on our Github
>
> https://github.com/orgs/BioSchemas/teams/blue-brain-nexus-knowledge-graph
>
> I await you all joining it and starting a discussion.
> I am also canvassing for a volunteer to lead the team
>
> Carole
>> I am interested in the discussion as well. How is this going to 
>> proceed? Is there some form thinkable where next to discussions, 
>> implementations are made to compare against?
>>
>> Cheers,
>>
>> Andra
>>
>> On Thu, Jan 4, 2018 at 1:18 PM, Philippe <proccaserra@gmail.com 
>> <mailto:proccaserra@gmail.com>> wrote:
>>
>>     Thank you Carole for circulating the link and MFSY for sending
>>     the information
>>     It seems that many people are interested. How do we want to get
>>     organized? What channel should we use for this interest group?
>>     this list ? a dedicated one?
>>
>>     all the best
>>
>>     Philippe
>>
>>     On 04/01/2018 02:40, Sarala Wimalaratne wrote:
>>>     Count me in…
>>>
>>>>     On 3 Jan 2018, at 17:14, Alejandra Gonzalez-Beltran
>>>>     <alejandra.gonzalezbeltran@oerc.ox.ac.uk
>>>>     <mailto:alejandra.gonzalezbeltran@oerc.ox.ac.uk>> wrote:
>>>>
>>>>     +1, I'm also interested in these topics. Tx!
>>>>
>>>>
>>>>     On 03/01/2018 17:12, Sy Mohameth François wrote:
>>>>>     Okay for me.
>>>>>     *From:*Justin Clark-Casey<justinccdev@gmail.com>
>>>>>     <mailto:justinccdev@gmail.com>
>>>>>     *Date:*Wednesday, 3 January 2018 at 18:09
>>>>>     *To:*Carole Goble<carole.goble@manchester.ac.uk>
>>>>>     <mailto:carole.goble@manchester.ac.uk>
>>>>>     *Cc:*BATISTA
>>>>>     Dominique<Dominique.BATISTA@france-bioinformatique.fr>
>>>>>     <mailto:Dominique.BATISTA@france-bioinformatique.fr>, Sy
>>>>>     Mohameth François<mohameth.sy@epfl.ch>
>>>>>     <mailto:mohameth.sy@epfl.ch>,"public-bioschemas@w3.org"
>>>>>     <mailto:public-bioschemas@w3.org><public-bioschemas@w3.org>
>>>>>     <mailto:public-bioschemas@w3.org>, Paolo
>>>>>     Missier<paolo.missier@newcastle.ac.uk>
>>>>>     <mailto:paolo.missier@newcastle.ac.uk>, Stian
>>>>>     Soiland-Reyes<soiland-reyes@manchester.ac.uk>
>>>>>     <mailto:soiland-reyes@manchester.ac.uk>,"pinarpink@yahoo.com"
>>>>>     <mailto:pinarpink@yahoo.com><pinarpink@yahoo.com>
>>>>>     <mailto:pinarpink@yahoo.com>, "Curcin,
>>>>>     Vasa"<vasa.curcin@kcl.ac.uk> <mailto:vasa.curcin@kcl.ac.uk>
>>>>>     *Subject:*Re: Blue Brain Nexus - A knowledge graph for
>>>>>     data-driven sciencehttps://bbp-nexus.epfl.ch/staging/docs/
>>>>>     <https://bbp-nexus.epfl.ch/staging/docs/>
>>>>>     Sounds good to me.
>>>>>     On Wed, Jan 3, 2018 at 4:54 PM, Carole Goble
>>>>>     <carole.goble@manchester.ac.uk
>>>>>     <mailto:carole.goble@manchester.ac.uk>> wrote:
>>>>>
>>>>>         Looks like we have our advocates!
>>>>>         Sy, Justin, Dominique (and Alasdair once he gets back
>>>>>         online!) how about convening a bioschemas developers
>>>>>         telcon to discuss ?
>>>>>         Best
>>>>>         Carole
>>>>>         *From:*BATISTA Dominique
>>>>>         [mailto:Dominique.BATISTA@france-bioinformatique.fr
>>>>>         <mailto:Dominique.BATISTA@france-bioinformatique.fr>]
>>>>>         *Sent:*03 January 2018 16:51
>>>>>         *To:*Justin Clark-Casey; Carole Goble
>>>>>         *Cc:*Sy Mohameth François;public-bioschemas@w3.org
>>>>>         <mailto:public-bioschemas@w3.org>; Paolo Missier; Stian
>>>>>         Soiland-Reyes;pinarpink@yahoo.com
>>>>>         <mailto:pinarpink@yahoo.com>; Curcin, Vasa
>>>>>         *Subject:*RE: Blue Brain Nexus - A knowledge graph for
>>>>>         data-driven sciencehttps://bbp-nexus.epfl.ch/staging/docs/
>>>>>         <https://bbp-nexus.epfl.ch/staging/docs/>
>>>>>         Hello,
>>>>>
>>>>>         Very interested aswell from a software developer point of
>>>>>         view, especially in terms of data validation and
>>>>>         exploitation of the ShEx and SHACL formats for various
>>>>>         purposes.
>>>>>         Definitely want to be part of that :)
>>>>>
>>>>>         Regards,
>>>>>         Dominique Batista
>>>>>         Web Engineer
>>>>>         CNRS - UMS3601
>>>>>         Phone:+33 01.69.82.46.92 <tel:+33%201%2069%2082%2046%2092>
>>>>>         Website:http://www.france-bioinformatique.fr
>>>>>         <http://www.france-bioinformatique.fr/>
>>>>>         ------------------------------------------------------------------------
>>>>>
>>>>>         *From:*Justin Clark-Casey [justinccdev@gmail.com
>>>>>         <mailto:justinccdev@gmail.com>]
>>>>>         *Sent:*Wednesday, January 03, 2018 5:43 PM
>>>>>         *To:*Carole Goble
>>>>>         *Cc:*Sy Mohameth François;public-bioschemas@w3.org
>>>>>         <mailto:public-bioschemas@w3.org>; Paolo Missier; Stian
>>>>>         Soiland-Reyes;pinarpink@yahoo.com
>>>>>         <mailto:pinarpink@yahoo.com>; Curcin, Vasa
>>>>>         *Subject:*Re: Blue Brain Nexus - A knowledge graph for
>>>>>         data-driven sciencehttps://bbp-nexus.epfl.ch/staging/docs/
>>>>>         <https://bbp-nexus.epfl.ch/staging/docs/>
>>>>>
>>>>>         Yes, I'm also very interested in SHACL / ShEx for
>>>>>         Bioschemas search engines and the like, and been reading
>>>>>         up a ton about knowledge graphs, etc. over the break, so
>>>>>         would be great to talk.
>>>>>
>>>>>         --
>>>>>         Justin Clark-Casey @justincc
>>>>>         Research Software Engineer
>>>>>         InterMine bio data integration platform
>>>>>         On Wed, Jan 3, 2018 at 4:35 PM, Carole Goble
>>>>>         <carole.goble@manchester.ac.uk
>>>>>         <mailto:carole.goble@manchester.ac.uk>> wrote:
>>>>>
>>>>>         Hello !
>>>>>
>>>>>         I am very interested in this work and not just for
>>>>>         Bioschemas...ResearchObject.org
>>>>>         <http://researchobject.org> are also looking to SHACL /
>>>>>         ShEx for representing complex manifests.
>>>>>
>>>>>         Once a few people are back from the holidays we should
>>>>>         pick up how to work together
>>>>>         Carole
>>>>>
>>>>>             Hi all,
>>>>>             Well I should start by saying that as the Blue Brain
>>>>>             Project Lead Knowledge Engineer [1], I’m part of the
>>>>>             team that design and develop the Blue Brain Nexus
>>>>>             platform.
>>>>>             The Nexus platform is an initiative from theBlue Brain
>>>>>             Project <https://bluebrain.epfl.ch/>(a Swiss
>>>>>             initiative for digitally reconstruct and simulate the
>>>>>             brain). It is adopted by Blue Brain and the European
>>>>>             Human Brain Project to support their data integration
>>>>>             effort in the context of neuroscience domain.
>>>>>             Schemas are expressed using W3C SHACL specification
>>>>>             within the Nexus platform. Any domain entity (not only
>>>>>             a neuroscience one) for which SHACL schemas is
>>>>>             produced can be managed in Nexus: CRUD operations on
>>>>>             SHACL schemas, validate instances against a schema,
>>>>>             CRUD operations on instances, store datasets,…
>>>>>             I’ve seen some discussions related to the usage of
>>>>>             SHACL or ShEx for validating Bioschemas profiles. In
>>>>>             case SHACL is chosen, Blue Brain Nexus may be a
>>>>>             potential candidate for testing schemas developed in
>>>>>             the context of Bioschemas.
>>>>>             The Neuroinformatics community is more and more
>>>>>             adopting Semantic Web technologies to model the
>>>>>             domains they are interested in.
>>>>>             Indeed many initiatives exist:
>>>>>                INCF:https://www.incf.org/which will host many
>>>>>             SHACL shapes for neuroscience related entities
>>>>>             (https://github.com/INCF/neuroshapes
>>>>>             <https://github.com/INCF/neuroshapes>)
>>>>>             NIF-Ontology:https://github.com/SciCrunch/NIF-Ontology
>>>>>             <https://github.com/SciCrunch/NIF-Ontology>where
>>>>>             standard neuroscience related ontologies are developed
>>>>>             and maintained.
>>>>>             Within Blue Brain project, schemas for many
>>>>>             neuroscience related entities (Subject, Neuron, Brain
>>>>>             Atlas,…) are being created, validated and managed
>>>>>             (checkout theBlue Brain schema repository
>>>>>             <https://github.com/BlueBrain/nexus-bbp-domains>to see
>>>>>             more examples). A SHACL schema example for a Subject
>>>>>             entity can be found
>>>>>             here:https://github.com/BlueBrain/nexus-bbp-domains/blob/master/modules/bbp-experiment/src/main/resources/schemas/bbp/experiment/subject/v0.1.0.json
>>>>>             <https://github.com/BlueBrain/nexus-bbp-domains/blob/master/modules/bbp-experiment/src/main/resources/schemas/bbp/experiment/subject/v0.1.0.json>and
>>>>>             an example of Subject instance can be found
>>>>>             here:https://github.com/BlueBrain/nexus-bbp-domains/blob/master/modules/bbp-experiment/src/test/resources/data/bbp/experiment/subject/v0.1.0/all-fields.json
>>>>>             <https://github.com/BlueBrain/nexus-bbp-domains/blob/master/modules/bbp-experiment/src/test/resources/data/bbp/experiment/subject/v0.1.0/all-fields.json>.
>>>>>             The above examples are not final and can be subject to
>>>>>             discussions.
>>>>>             Of course, a first step when creating schemas is to
>>>>>             look at what exist out there for reuse/extension
>>>>>             purpose. That’s why we’re very interested on
>>>>>             initiative like Bioschemas.
>>>>>             The point here is to bootstrap a discussion to see if
>>>>>             the Bioschemas community is interesting in
>>>>>             endorsing/getting involved/supporting neuroscience
>>>>>             related entity description standardisation. Subject
>>>>>             entity can be a good start. The neuroscience community
>>>>>             should be involved as well at some point.
>>>>>             Cheers
>>>>>             MFSY.
>>>>>             [1]:https://bluebrain.epfl.ch/page-143719-en.html
>>>>>             <https://bluebrain.epfl.ch/page-143719-en.html>
>>>>>             *From:*Carole Goble<carole.goble@manchester.ac.uk>
>>>>>             <mailto:carole.goble@manchester.ac.uk>
>>>>>             *Date:*Wednesday, 3 January 2018 at 16:00
>>>>>             *To:*"public-bioschemas@w3.org"
>>>>>             <mailto:public-bioschemas@w3.org><public-bioschemas@w3.org>
>>>>>             <mailto:public-bioschemas@w3.org>
>>>>>             *Cc:*Paolo Missier<paolo.missier@newcastle.ac.uk>
>>>>>             <mailto:paolo.missier@newcastle.ac.uk>, Stian
>>>>>             Soiland-Reyes<soiland-reyes@manchester.ac.uk>
>>>>>             <mailto:soiland-reyes@manchester.ac.uk>,"pinarpink@yahoo.com"
>>>>>             <mailto:pinarpink@yahoo.com><pinarpink@yahoo.com>
>>>>>             <mailto:pinarpink@yahoo.com>,"carole.goble@manchester.ac.uk"
>>>>>             <mailto:carole.goble@manchester.ac.uk><carole.goble@manchester.ac.uk>
>>>>>             <mailto:carole.goble@manchester.ac.uk>, "Curcin,
>>>>>             Vasa"<vasa.curcin@kcl.ac.uk>
>>>>>             <mailto:vasa.curcin@kcl.ac.uk>
>>>>>             *Subject:*Blue Brain Nexus - A knowledge graph for
>>>>>             data-driven
>>>>>             sciencehttps://bbp-nexus.epfl.ch/staging/docs/
>>>>>             <https://bbp-nexus.epfl.ch/staging/docs/>
>>>>>             *Resent-From:*<public-bioschemas@w3.org>
>>>>>             <mailto:public-bioschemas@w3.org>
>>>>>             *Resent-Date:*Wednesday, 3 January 2018 at 15:58
>>>>>
>>>>>             Just saw this tweeted....
>>>>>
>>>>>             https://github.com/BlueBrain/nexus
>>>>>             <https://github.com/BlueBrain/nexus>
>>>>>
>>>>>
>>>>>               Blue Brain Nexus - A knowledge graph for data-driven
>>>>>               science
>>>>>
>>>>>             The Blue Brain Nexus is a provenance based, semantic
>>>>>             enabled data management platform enabling the
>>>>>             definition of an arbitrary domain of application for
>>>>>             which there is a need to create and manage entities as
>>>>>             well as their relations (e.g. provenance). For
>>>>>             example, the domain of application managed by the
>>>>>             Nexus platform deployed at Blue Brain is to digitally
>>>>>             reconstruct and simulate the brain.
>>>>>
>>>>>             At the heart of the Blue Brain Nexus platform lies the
>>>>>             Knowledge Graph, at Blue Brain, it will allow
>>>>>             scientists to:
>>>>>
>>>>>              1. Register and manage neuroscience relevant entity
>>>>>                 types through schemas that can reuse or extend
>>>>>                 community defined schemas (e.g.schema.org
>>>>>                 <http://schema.org/>,*bioschema.org
>>>>>                 <http://bioschema.org/>*, W3C-PROV) and ontologies
>>>>>                 (e.g. brain parcellation schemes, cell types,
>>>>>                 taxonomy).
>>>>>              2. Submit data to the platform and describe their
>>>>>                 provenance using the W3C PROV model. Provenance is
>>>>>                 about how data or things are generated (e.g.
>>>>>                 protocols, methods used...), when (e.g. timeline)
>>>>>                 and by whom (e.g. people, software...). Provenance
>>>>>                 supports the data reliability and quality
>>>>>                 assessment as well as enables workflow
>>>>>                 reproducibility. Platform users can submit data
>>>>>                 either through web forms or programmatic interfaces.
>>>>>              3. Search, discover, reuse and derive high-quality
>>>>>                 neuroscience data generated within and outside the
>>>>>                 platform for the purpose of driving their own
>>>>>                 scientific endeavours. Data can be examined by
>>>>>                 species, contributing laboratory, methodology,
>>>>>                 brain region, and data type, thereby allowing
>>>>>                 functionality not currently available elsewhere.
>>>>>                 The data are predominantly organized into atlases
>>>>>                 (e.g. Allen CCF, Waxholm) and linked to the
>>>>>                 KnowledgeSpace – a collaborative community-based
>>>>>                 encyclopedia linking brain research concepts to
>>>>>                 the latest data, models and literature.
>>>>>
>>>>>             It is to be noted that many other scientific fields
>>>>>             (Astronomy, Agriculture, Bioinformatics,
>>>>>             Pharmaceutical industry, ...) are in need of such a
>>>>>             technology. Consequently, Blue Brain Nexus core
>>>>>             technology is being developed to be*agnostic of the
>>>>>             domain*it might be applied to.
>>>>>
>>>>>             -- 
>>>>>
>>>>>             Professor Carole Goble CBE FREng FBCS CITP
>>>>>
>>>>>             School of Computer Science
>>>>>
>>>>>             The University of Manchester
>>>>>
>>>>>             Manchester, UK
>>>>>
>>>>>             tel: +44 161 275 6195 <tel:+44%20161%20275%206195>
>>>>>
>>>>>             email: carole.goble@manchester.ac.uk
>>>>>             <mailto:carole.goble@manchester.ac.uk>
>>>>>
>>>>>             twitter: @CaroleAnneGoble
>>>>>
>>>>>             PLEASE NOTE: I no longer work weekends. You will not
>>>>>             get a response.
>>>>>
>>>>>             email etiquette:
>>>>>
>>>>>             I get a lot of email and when I travel it gets even
>>>>>             more backed up.
>>>>>
>>>>>             - Don't get too upset if my replies are short (see
>>>>>             http://www.phdcomics.com/comics/archive.php?comicid=1047
>>>>>             <http://www.phdcomics.com/comics/archive.php?comicid=1047>)
>>>>>
>>>>>             - If you don't get a reply within 48 hours there is a
>>>>>             good chance the email has scrolled into the distance.
>>>>>             If its urgent try again or email
>>>>>             melanie.price@manchester.ac.uk
>>>>>             <mailto:melanie.price@manchester.ac.uk>.
>>>>>
>>>>>             If you haven't heard within a week you really should
>>>>>             try again.
>>>>>
>>>>>         -- 
>>>>>
>>>>>         Professor Carole Goble CBE FREng FBCS CITP
>>>>>
>>>>>         School of Computer Science
>>>>>
>>>>>         The University of Manchester
>>>>>
>>>>>         Manchester, UK
>>>>>
>>>>>         tel: +44 161 275 6195 <tel:+44%20161%20275%206195>
>>>>>
>>>>>         email: carole.goble@manchester.ac.uk
>>>>>         <mailto:carole.goble@manchester.ac.uk>
>>>>>
>>>>>         twitter: @CaroleAnneGoble
>>>>>
>>>>>         PLEASE NOTE: I no longer work weekends. You will not get a
>>>>>         response.
>>>>>
>>>>>         email etiquette:
>>>>>
>>>>>         I get a lot of email and when I travel it gets even more
>>>>>         backed up.
>>>>>
>>>>>         - Don't get too upset if my replies are short (see
>>>>>         http://www.phdcomics.com/comics/archive.php?comicid=1047
>>>>>         <http://www.phdcomics.com/comics/archive.php?comicid=1047>)
>>>>>
>>>>>         - If you don't get a reply within 48 hours there is a good
>>>>>         chance the email has scrolled into the distance. If its
>>>>>         urgent try again or email melanie.price@manchester.ac.uk
>>>>>         <mailto:melanie.price@manchester.ac.uk>.
>>>>>
>>>>>         If you haven't heard within a week you really should try
>>>>>         again.
>>>>>
>>>>
>>>>
>>>
>>
>>
>
> -- 
> Professor Carole Goble CBE FREng FBCS CITP
> School of Computer Science
> The University of Manchester
> Manchester, UK
>
> tel: +44 161 275 6195
> email:carole.goble@manchester.ac.uk
> twitter: @CaroleAnneGoble
>
> PLEASE NOTE: I no longer work weekends. You will not get a response.
>
> email etiquette:
> I get a lot of email and when I travel it gets even more backed up.
>
> - Don't get too upset if my replies are short (seehttp://www.phdcomics.com/comics/archive.php?comicid=1047)
> - If you don't get a reply within 48 hours there is a good chance the email has scrolled into the distance. If its urgent try again or emailmelanie.price@manchester.ac.uk.
> If you haven't heard within a week you really should try again.
Received on Monday, 15 January 2018 11:21:24 UTC

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