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

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Thu, 4 Jan 2018 13:44:38 +0000
To: 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>, carole.goble@manchester.ac.uk
Message-ID: <7dff329d-05cb-ae3a-d3dc-383f367de43c@manchester.ac.uk>


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 (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.
Received on Thursday, 4 January 2018 13:45:05 UTC

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