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

From: Philippe <proccaserra@gmail.com>
Date: Thu, 4 Jan 2018 12:18:38 +0000
To: Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>
Cc: Sy Mohameth François <mohameth.sy@epfl.ch>, Justin Clark-Casey <justinccdev@gmail.com>, Carole Goble <carole.goble@manchester.ac.uk>, 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: <286a0f6e-5a4f-2608-9e55-ef91dc909d39@gmail.com>
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>
>>> *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 
>>> sciencehttps://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/
>>>     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/
>>>
>>>     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)
>>>         NIF-Ontology:https://github.com/SciCrunch/NIF-Ontologywhere
>>>         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.jsonand
>>>         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 sciencehttps://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 Thursday, 4 January 2018 12:19:07 UTC

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