- From: Carole Goble <carole.goble@manchester.ac.uk>
- Date: Mon, 15 Jan 2018 11:25:39 +0000
- To: Leyla Garcia <ljgarcia@ebi.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: <0700c2e5-6376-e99c-5253-df8b12306c90@manchester.ac.uk>
Hi Andra and Dom are leading...Dom should be able to invite you :-) Carole > 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. > > -- Professor Carole Goble CBE FREng FBCS CITP School of Computer Science University of Manchester Manchester, UK tel: +44 161 275 6195 email: carole.goble@manchester.ac.uk twitter: @CaroleAnneGoble PA: Melanie Price <melanie.j.price@manchester.ac.uk> 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 Monday, 15 January 2018 11:26:05 UTC