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

From: Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>
Date: Tue, 9 Jan 2018 10:25:15 +0000
To: Andra Waagmeester <andra@micelio.be>
CC: Pinar Alper <pinarpink@yahoo.com>, 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>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>
Message-ID: <aa26b726-aa24-477f-950b-95311a7ddb58@email.android.com>
Great!

I have the paper edition of the book on my desk, it is really well written and easy to follow.

On 7 Jan 2018 4:05 pm, Andra Waagmeester <andra@micelio.be> wrote:
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<mailto: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<mailto: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<mailto: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<mailto:Paolo.Missier@newcastle.ac.uk>, pmissier@acm.org<mailto: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<mailto: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<mailto: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<mailto:carole.goble@manchester.ac.uk> >

Date: Thursday, 4 January 2018 at 14:44
To: Andra Waagmeester <andra@micelio.be<mailto:andra@micelio.be>>, Philippe <proccaserra@gmail.com<mailto:proccaserra@gmail.com>>
Cc: Sarala Wimalaratne <sarala@ebi.ac.uk<mailto:sarala@ebi.ac.uk>>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oer c.ox.ac.uk<mailto:alejandra.gonzalezbeltran@oerc.ox.ac.uk>>, Sy Mohameth François <mohameth.sy@epfl.ch<mailto:mohameth.sy@epfl.ch>>, Justin Clark-Casey <justinccdev@gmail.com<mailto:justinccdev@gmail.com>>, BATISTA Dominique <Dominique.BATISTA@france-bioi nformatique.fr<mailto:Dominique.BATISTA@france-bioinformatique.fr>>, "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.u k<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>>, "carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk> " <carole.goble@manchester.ac.uk<mailto: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<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@oer c.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@f rance-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@newcastl e.ac.uk><mailto:paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@m anchester.ac.uk><mailto:soiland-reyes@manchester.ac.uk>, "pinarpink@y ahoo.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 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<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@fran ce-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 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<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 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<mailto: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><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@newcast le.ac.uk><mailto:paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@m anchester.ac.uk><mailto:soiland-reyes@manchester.ac.uk>, "pinarpink@y ahoo.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 science https://bbp-nexus.epfl .ch/staging/docs/<https://bbp-nexus.epfl.ch/staging/docs/>
Resent-From: <public-bioschema s@w3.org><mailto: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<http://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<mailto:carole.goble@manchester.ac.uk>

twitter: @CaroleAnneGoble



PLEASE NOTE: I no longer work weekends. You will not get a response.



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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<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/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<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<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/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<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)
- 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.



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