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

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/ <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 
> <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>
> *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....
>
> 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*, 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
> 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 (seehttp://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 emailmelanie.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.