- From: Leyla Garcia <ljgarcia@ebi.ac.uk>
- Date: Mon, 15 Jan 2018 11:20:56 +0000
- To: Carole Goble <carole.goble@manchester.ac.uk>, Andra Waagmeester <andra@micelio.be>, Philippe <proccaserra@gmail.com>
- Cc: Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>, Sy Mohameth François <mohameth.sy@epfl.ch>, 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: <65b3ca90-2a8d-868a-4cc6-f4d55d45f608@ebi.ac.uk>
Hi Carole, Sorry about my late response. Could you please invite me to join the group? If you are still looking for volunteers to lead the group, I could help (maybe). Just please give me some more days to go through the emails and see how I could contribute. I am still away this week so do not expect to catch up before next week. Regards, On 04/01/2018 13:44, Carole Goble wrote: > > > > Andra > I started up a bioschemas team on our Github > > 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 (see >>>>> http://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 email >>>>> melanie.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 (see >>>>> http://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 email melanie.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 (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. > If you haven't heard within a week you really should try again.
Received on Monday, 15 January 2018 11:21:24 UTC