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: Justin Clark-Casey <justinccdev@gmail.com>
Date: Wed, 3 Jan 2018 16:43:40 +0000
Message-ID: <CAME9NR_r1V6JdsCRynrOodRf9zU1ugkSbGnPnmDJoGgpke0rGA@mail.gmail.com>
To: Carole Goble <carole.goble@manchester.ac.uk>
Cc: 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>
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>
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>
> <carole.goble@manchester.ac.uk>
> *Date: *Wednesday, 3 January 2018 at 16:00
> *To: *"public-bioschemas@w3.org" <public-bioschemas@w3.org>
> <public-bioschemas@w3.org> <public-bioschemas@w3.org>
> *Cc: *Paolo Missier <paolo.missier@newcastle.ac.uk>
> <paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes
> <soiland-reyes@manchester.ac.uk> <soiland-reyes@manchester.ac.uk>,
> "pinarpink@yahoo.com" <pinarpink@yahoo.com> <pinarpink@yahoo.com>
> <pinarpink@yahoo.com>, "carole.goble@manchester.ac.uk"
> <carole.goble@manchester.ac.uk> <carole.goble@manchester.ac.uk>
> <carole.goble@manchester.ac.uk>, "Curcin, Vasa" <vasa.curcin@kcl.ac.uk>
> <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> <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, *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 <+44%20161%20275%206195>
>
> 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.
>
>
> --
> Professor Carole Goble CBE FREng FBCS CITP
> School of Computer Science
> The University of Manchester
> Manchester, UK
>
> tel: +44 161 275 6195 <+44%20161%20275%206195>
> 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 Wednesday, 3 January 2018 16:44:05 UTC

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