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

From: Andra Waagmeester <andra@micelio.be>
Date: Sun, 7 Jan 2018 17:05:04 +0100
Message-ID: <CAMNM0fWhqqAYa5o=82-Lq15v0r4P-J1r9KF4KC87hDDXySubBg@mail.gmail.com>
To: Pinar Alper <pinarpink@yahoo.com>
Cc: Carole Goble <carole.goble@manchester.ac.uk>, "Clark, Timothy W." <TWCLARK@mgh.harvard.edu>, Paolo Missier <paolo.missier@newcastle.ac.uk>, Sy Mohameth François <mohameth.sy@epfl.ch>, Philippe <proccaserra@gmail.com>, Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>, Justin Clark-Casey <justinccdev@gmail.com>, BATISTA Dominique <Dominique.BATISTA@france-bioinformatique.fr>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>
The html version of the book "validating RDF" is now available as HTML:
http://book.validatingrdf.com/

This might be of interest for this group.

Cheers,

Andra

On Fri, Jan 5, 2018 at 6:45 PM, Pinar Alper <pinarpink@yahoo.com> wrote:

> Hi Carole,
>
>
> I would like to join aswell
>
> regards
> pinar
>
> On Friday, January 5, 2018, 4:13:27 PM GMT+1, Clark, Timothy W. <
> TWCLARK@mgh.harvard.edu> wrote:
>
>
> That is precisely my interest as well.
>
> On Jan 5, 2018, at 4:52 AM, Paolo Missier <paolo.missier@newcastle.ac.uk>
> wrote:
>
> Hi Carole, I am specifically interested in how BlueBrains embeds PROV in
> its schemas and especially what comes out at the other end as tangible
> benefit to neuroscientists — I heard a talk long ago where this was
> mentioned (at some RDA IG perhaps?) but just in passing.
> So if this is the right forum to learn more on this then I’d love to join,
> even just to listen in
>
> Cheers,
>   —Paolo
>
> ==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-
> ==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-==-
> Dr. Paolo Missier http://tinyurl.com/paolomissier
> Reader in Large-scale Information Management
> Paolo.Missier@newcastle.ac.uk, pmissier@acm.org
> School of Computing LinkedIn: http://uk.linkedin.com/pub/paolo-missier
> Newcastle University,  UK Twitter: @PMissier
> Urban Sciences Building Photography: http://scattidistratti.smugmug.com/
> Newcastle upon Tyne, NE4 5TG http://missier.it
> =- Observe, Interpret, Understand, Act. Repeat -=
>
> On 4 Jan 2018, at 14:24, Carole Goble <carole.goble@manchester.ac.uk>
> wrote:
>
>
> Hi
> I have invited all who responded - At least I think I have!
> I have also made Dom the owner
>
> Carole
>
> I would be interested in these discussions too. I think the Bioschema
> admins would have to invite members to join and add these members to the
> team itself. Looking forward to the invite link.
>
> § Susheel
>
>
> On 4 January 2018 at 14:11, Sy Mohameth François <mohameth.sy@epfl.ch>
> wrote:
>
> A bioschemas team for BlueBrain Nexus sounds good.
>
>
> I didn’t receive an invitation to join the team and the link looks broken
> (or only team member can see its content). Can I be invited to join the
> team ?
>
> I would prefer someone else to lead this team as I’m part of the BlueBrain
> Nexus. But If no one volunteered (and if feasible as I don’t know the rules
> in the Bioschemas community) I would be happy to lead it.
>
>
> Cheers
>
> MFSY.
>
>
> *From: *Carole Goble <carole.goble@manchester.ac.uk >
>
> *Date: *Thursday, 4 January 2018 at 14:44
> *To: *Andra Waagmeester <andra@micelio.be>, Philippe <
> proccaserra@gmail.com>
> *Cc: *Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oer
> c.ox.ac.uk <alejandra.gonzalezbeltran@oerc.ox.ac.uk>>, Sy Mohameth
> François <mohameth.sy@epfl.ch>, Justin Clark-Casey <justinccdev@gmail.com>,
> BATISTA Dominique <Dominique.BATISTA@france-bioi nformatique.fr
> <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.u k
> <soiland-reyes@manchester.ac.uk>>, "pinarpink@yahoo.com" <
> pinarpink@yahoo.com>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>, "
> carole.goble@manchester.ac.uk " <carole.goble@manchester.ac.uk >
>
>
> *Subject: *Re: Blue Brain Nexus - A knowledge graph for data-driven
> science https://bbp-nexus.epfl.ch/stag ing/docs/
> <https://bbp-nexus.epfl.ch/staging/docs/>
>
>
>
>
> Andra
> I started up a bioschemas team on our Github
>
> https://github.com/orgs/BioSch emas/teams/blue-brain-nexus- knowledge-graph
> <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> 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@oer
> c.ox.ac.uk <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>
> <justinccdev@gmail.com>
> *Date: *Wednesday, 3 January 2018 at 18:09
> *To: *Carole Goble <carole.goble@manchester .ac.uk>
> <carole.goble@manchester.ac.uk>
> *Cc: *BATISTA Dominique <Dominique.BATISTA@f rance-bioinformatique.fr>
> <Dominique.BATISTA@france-bioinformatique.fr>, Sy Mohameth François
> <mohameth.sy@epfl.ch> <mohameth.sy@epfl.ch> , "public-bioschemas@w3.org"
> <public-bioschemas@w3.org> < public-bioschemas@w3.org>
> <public-bioschemas@w3.org>, Paolo Missier<paolo.missier@newcastl e.ac.uk>
> <paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@m
> anchester.ac.uk> <soiland-reyes@manchester.ac.uk>, "pinarpink@y ahoo.com"
> <pinarpink@yahoo.com> <pinarpink@yahoo.com > <pinarpink@yahoo.com>,
> "Curcin, Vasa" <vasa.curcin@kcl.ac.uk> <vasa.curcin@kcl.ac.uk>
> *Subject: *Re: Blue Brain Nexus - A knowledge graph for data-driven
> science https://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 > 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@fran
> ce-bioinformatique.fr <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
> <public-bioschemas@w3.org>; Paolo Missier; Stian Soiland-Reyes; pinarpink@yahoo
> .com <pinarpink@yahoo.com>; Curcin, Vasa
> *Subject:* RE: Blue Brain Nexus - A knowledge graph for data-driven
> science https://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
> Website: http://www.france-bio informatique.fr
> <http://www.france-bioinformatique.fr/>
> ------------------------------
>
> *From:* Justin Clark-Casey [justinccdev@gmail.com]
> *Sent:* Wednesday, January 03, 2018 5:43 PM
> *To:* Carole Goble
> *Cc:* Sy Mohameth François; public-bioschemas@w3 .org
> <public-bioschemas@w3.org>; Paolo Missier; Stian Soiland-Reyes; pinarpink@yahoo
> .com <pinarpink@yahoo.com>; Curcin, Vasa
> *Subject:* Re: Blue Brain Nexus - A knowledge graph for data-driven
> science https://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 > wrote:
>
>
> Hello !
>
> I am very interested in this work and not just for Bioschemas...ResearchObject.or
> g <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 the Blue 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/neuro shapes
> <https://github.com/INCF/neuroshapes>)
>
>    NIF-Ontology: https://githu b.com/SciCrunch/NIF-Ontology
> <https://github.com/SciCrunch/NIF-Ontology> w here 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 the Blue 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/BlueB
> rain/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/BlueB
> rain/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>
> <carole.goble@manchester.ac.uk>
> *Date: *Wednesday, 3 January 2018 at 16:00
> *To: *"public-bioschemas@w3.org" <public-bioschemas@w3.org>
> <public-bioschemas@w3.org> <public-bioschemas@w3.org>
> *Cc: *Paolo Missier <paolo.missier@newcast le.ac.uk>
> <paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@m
> anchester.ac.uk> <soiland-reyes@manchester.ac.uk>, "pinarpink@y ahoo.com"
> <pinarpink@yahoo.com> <pinarpink@yahoo.com > <pinarpink@yahoo.com>, "carole.goble@manchester.
> ac.uk" <carole.goble@manchester.ac.uk><carole.goble@ manchester.ac.uk>
> <carole.goble@manchester.ac.uk>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>
> <vasa.curcin@kcl.ac.uk>
> *Subject: *Blue Brain Nexus - A knowledge graph for data-driven science https://bbp-nexus.epfl
> .ch/staging/docs/ <https://bbp-nexus.epfl.ch/staging/docs/>
> *Resent-From: *<public-bioschema s@w3.org> <public-bioschemas@w3.org>
> *Resent-Date: *Wednesday, 3 January 2018 at 15:58
>
>
>
> Just saw this tweeted....
>
> https://github.com/BlueBrain/n exus <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, *bioschema.or g <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
>
> 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 (see http://www.phdcomics.com/comic s/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 .
>
> 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 (see http://www.phdcomics.com/comic s/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 .
>
> 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 (see http://www.phdcomics.com/comic s/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 .
>
> 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 <+44%20161%20275%206195>
> 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 (see 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.
> If you haven't heard within a week you really should try again.
>
>
>
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Received on Sunday, 7 January 2018 16:07:06 UTC

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