W3C home > Mailing lists > Public > public-bioschemas@w3.org > January 2018

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 12:48:07 +0000
To: Philippe <proccaserra@gmail.com>, 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>, 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: <5571ec5c-4fc1-4a9e-2163-553dca276057@manchester.ac.uk>

I would like us to use the Bioschemas.org channels

I suggest a team
https://github.com/orgs/BioSchemas/teams
be set up.

Who would like to volunteer as team leader?

Carole

> 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.
>>>>
>>>
>>>
>>
>

-- 
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 12:48:30 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 19:08:01 UTC