- From: Carole Goble <carole.goble@manchester.ac.uk>
- Date: Thu, 4 Jan 2018 14:24:57 +0000
- To: susheel.varma@ebi.ac.uk, Sy Mohameth François <mohameth.sy@epfl.ch>
- Cc: Andra Waagmeester <andra@micelio.be>, Philippe <proccaserra@gmail.com>, Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>, 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>
- Message-ID: <14768fa1-890c-fcf1-aa85-95c990baada2@manchester.ac.uk>
Hi I have invited all who responded - At least I think I have! I have also made Dom the owner Carole > I would be interested in these discussions too. I think the Bioschema > admins would have to invite members to join and add these members to > the team itself. Looking forward to the invite link. > > § Susheel > > > On 4 January 2018 at 14:11, Sy Mohameth François <mohameth.sy@epfl.ch > <mailto:mohameth.sy@epfl.ch>> wrote: > > A bioschemas team for BlueBrain Nexus sounds good. > > I didn’t receive an invitation to join the team and the link looks > broken (or only team member can see its content). Can I be invited > to join the team ? > > I would prefer someone else to lead this team as I’m part of the > BlueBrain Nexus. But If no one volunteered (and if feasible as I > don’t know the rules in the Bioschemas community) I would be happy > to lead it. > > Cheers > > MFSY. > > *From: *Carole Goble <carole.goble@manchester.ac.uk > <mailto:carole.goble@manchester.ac.uk>> > *Date: *Thursday, 4 January 2018 at 14:44 > *To: *Andra Waagmeester <andra@micelio.be > <mailto:andra@micelio.be>>, Philippe <proccaserra@gmail.com > <mailto:proccaserra@gmail.com>> > *Cc: *Sarala Wimalaratne <sarala@ebi.ac.uk > <mailto:sarala@ebi.ac.uk>>, Alejandra Gonzalez-Beltran > <alejandra.gonzalezbeltran@oerc.ox.ac.uk > <mailto:alejandra.gonzalezbeltran@oerc.ox.ac.uk>>, Sy Mohameth > François <mohameth.sy@epfl.ch <mailto:mohameth.sy@epfl.ch>>, > Justin Clark-Casey <justinccdev@gmail.com > <mailto:justinccdev@gmail.com>>, BATISTA Dominique > <Dominique.BATISTA@france-bioinformatique.fr > <mailto:Dominique.BATISTA@france-bioinformatique.fr>>, > "public-bioschemas@w3.org <mailto:public-bioschemas@w3.org>" > <public-bioschemas@w3.org <mailto:public-bioschemas@w3.org>>, > 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>>, "Curcin, Vasa" > <vasa.curcin@kcl.ac.uk <mailto:vasa.curcin@kcl.ac.uk>>, > "carole.goble@manchester.ac.uk > <mailto:carole.goble@manchester.ac.uk>" > <carole.goble@manchester.ac.uk <mailto:carole.goble@manchester.ac.uk>> > > > *Subject: *Re: Blue Brain Nexus - A knowledge graph for > data-driven science https://bbp-nexus.epfl.ch/staging/docs/ > <https://bbp-nexus.epfl.ch/staging/docs/> > > Andra > I started up a bioschemas team on our Github > > https://github.com/orgs/BioSchemas/teams/blue-brain-nexus-knowledge-graph > <https://github.com/orgs/BioSchemas/teams/blue-brain-nexus-knowledge-graph> > > I await you all joining it and starting a discussion. > I am also canvassing for a volunteer to lead the team > > Carole > > I am interested in the discussion as well. How is this going > to proceed? Is there some form thinkable where next to > discussions, implementations are made to compare against? > > Cheers, > > Andra > > On Thu, Jan 4, 2018 at 1:18 PM, Philippe > <proccaserra@gmail.com <mailto:proccaserra@gmail.com>> wrote: > > 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> > <mailto:justinccdev@gmail.com> > *Date:*Wednesday, 3 January 2018 at 18:09 > *To:*Carole > Goble<carole.goble@manchester.ac.uk> > <mailto:carole.goble@manchester.ac.uk> > *Cc:*BATISTA > Dominique<Dominique.BATISTA@france-bioinformatique.fr> > <mailto:Dominique.BATISTA@france-bioinformatique.fr>, > Sy Mohameth François<mohameth.sy@epfl.ch> > <mailto:mohameth.sy@epfl.ch>,"public-bioschemas@w3.org" > <mailto:public-bioschemas@w3.org><public-bioschemas@w3.org> > <mailto:public-bioschemas@w3.org>, 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>, "Curcin, > Vasa"<vasa.curcin@kcl.ac.uk> > <mailto:vasa.curcin@kcl.ac.uk> > *Subject:*Re: Blue Brain Nexus - A knowledge > graph for data-driven > sciencehttps://bbp-nexus.epfl.ch/staging/docs/ > <https://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/ > <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 > <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/ > <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 > <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 > <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 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.json > <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 > <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 > <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/ > <https://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 > <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 (seehttp://www.phdcomics.com/comics/archive.php?comicid=1047 > <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 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 <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 (seehttp://www.phdcomics.com/comics/archive.php?comicid=1047 > <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 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 <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 (seehttp://www.phdcomics.com/comics/archive.php?comicid=1047 > <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 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.
Received on Thursday, 4 January 2018 14:25:22 UTC