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

From: Sy Mohameth François <mohameth.sy@epfl.ch>
Date: Wed, 3 Jan 2018 16:27:43 +0000
To: Carole Goble <carole.goble@manchester.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
CC: 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: <B05C7336-75CD-4575-8420-CD46E087FD56@epfl.ch>
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.


[1]: https://bluebrain.epfl.ch/page-143719-en.html

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Wednesday, 3 January 2018 at 16:00
To: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Cc: Paolo Missier <paolo.missier@newcastle.ac.uk>, Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>, "pinarpink@yahoo.com" <pinarpink@yahoo.com>, "carole.goble@manchester.ac.uk" <carole.goble@manchester.ac.uk>, "Curcin, Vasa" <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>
Resent-Date: Wednesday, 3 January 2018 at 15:58

Just saw this tweeted....


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, 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

email: carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk>

twitter: @CaroleAnneGoble

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Received on Wednesday, 3 January 2018 16:28:11 UTC

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