- From: Carole Goble <carole.goble@manchester.ac.uk>
- Date: Thu, 4 Jan 2018 12:48:07 +0000
- To: Philippe <proccaserra@gmail.com>, Sarala Wimalaratne <sarala@ebi.ac.uk>, Alejandra Gonzalez-Beltran <alejandra.gonzalezbeltran@oerc.ox.ac.uk>
- Cc: 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>, carole.goble@manchester.ac.uk
- Message-ID: <5571ec5c-4fc1-4a9e-2163-553dca276057@manchester.ac.uk>
I would like us to use the Bioschemas.org channels I suggest a team https://github.com/orgs/BioSchemas/teams be set up. Who would like to volunteer as team leader? Carole > 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> >>>> *Date:*Wednesday, 3 January 2018 at 18:09 >>>> *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> >>>> *Subject:*Re: Blue Brain Nexus - A knowledge graph for data-driven >>>> sciencehttps://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/ >>>> 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/ >>>> >>>> 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) >>>> NIF-Ontology:https://github.com/SciCrunch/NIF-Ontologywhere >>>> 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.jsonand >>>> 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> >>>> <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/ >>>> *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 >>>> >>>> >>>> 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) >>>> >>>> - 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) >>>> >>>> - 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 (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 12:48:30 UTC