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

From: Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>
Date: Wed, 3 Jan 2018 17:14:16 +0000
To: Sy Mohameth François <mohameth.sy@epfl.ch>, Justin Clark-Casey <justinccdev@gmail.com>, Carole Goble <carole.goble@manchester.ac.uk>
Cc: 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: <f3f708b3-5adc-6d11-093f-db99f6572e56@oerc.ox.ac.uk>
+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>
> *Date: *Wednesday, 3 January 2018 at 18:09
> *To: *Carole Goble <carole.goble@manchester.ac.uk>
> *Cc: *BATISTA Dominique <Dominique.BATISTA@france-bioinformatique.fr>, 
> Sy Mohameth François <mohameth.sy@epfl.ch>, "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>
> *Subject: *Re: Blue Brain Nexus - A knowledge graph for data-driven 
> science 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 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 <tel:+33%201%2069%2082%2046%2092>
>     Website: 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/
>
>     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 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/neuroshapes)
>
>         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 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/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.
>
>
>         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
>
>         *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 science 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
>
>
>           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)
>
>         - 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.
>
Received on Wednesday, 3 January 2018 17:14:48 UTC

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