- From: Justin Clark-Casey <justinccdev@gmail.com>
- Date: Wed, 3 Jan 2018 17:09:36 +0000
- 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>
- Message-ID: <CAME9NR-JeSQ+xwkkJJjwLHYAOCMuzaxQOtFh5VuRFcj-=QzTFQ@mail.gmail.com>
Sounds good to me. On Wed, Jan 3, 2018 at 4:54 PM, Carole Goble <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] > *Sent:* 03 January 2018 16:51 > *To:* Justin Clark-Casey; Carole Goble > *Cc:* Sy Mohameth François; public-bioschemas@w3.org; Paolo Missier; > Stian Soiland-Reyes; pinarpink@yahoo.com; Curcin, Vasa > *Subject:* RE: Blue Brain Nexus - A knowledge graph for data-driven > science https://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 <+33%201%2069%2082%2046%2092> > Website: http://www.france-bioinformatique.fr > ------------------------------ > > *From:* Justin Clark-Casey [justinccdev@gmail.com] > *Sent:* Wednesday, January 03, 2018 5:43 PM > *To:* Carole Goble > *Cc:* Sy Mohameth François; public-bioschemas@w3.org; Paolo Missier; > Stian Soiland-Reyes; pinarpink@yahoo.com; Curcin, Vasa > *Subject:* Re: Blue Brain Nexus - A knowledge graph for data-driven > science https://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> 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 17:10:07 UTC