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From: <su...@eb...> - 2018-10-26 11:10:31
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This is a forward of transaction #5741098 of ticket #305112 |
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From: Dani W. <dw...@eb...> - 2018-08-15 09:56:28
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Dear EFO users, EFO version 2.99 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. Thank you very much, Dani Welter, PhD Ontologist, Human Cell Atlas Samples, Phenotypes and Ontologies Team --------------------------------------- European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0) 1223 492 502 |
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From: Zoe M. P. <zm...@eb...> - 2018-06-18 09:05:56
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Dear EFO users, EFO version 2.97 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, Zoë May Pendlington |
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From: Zoe M. P. <zm...@eb...> - 2018-05-15 09:25:39
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Dear EFO users, EFO version 2.96 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, Zoë May Pendlington |
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From: Paola R. <pa...@eb...> - 2018-04-16 09:22:08
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Dear EFO users, EFO version 2.95 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, -- Paola Roncaglia, PhD European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 492600 Fax: +44 1223 494468 |
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From: Dani W. <dw...@eb...> - 2018-03-15 10:37:14
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Dear EFO users, EFO version 2.94 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, Dani Welter, PhD Ontologist/Bioinformatician Samples, Phenotypes and Ontologies Team --------------------------------------- European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0) 1223 492 502 |
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From: Dani W. <dw...@eb...> - 2018-02-15 23:20:34
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Dear EFO users, EFO version 2.93 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users We are projecting to freeze communications via efo...@li... by mid 2018. ================================================ Thank you very much, Dani Welter, PhD Ontologist/Bioinformatician Samples, Phenotypes and Ontologies Team --------------------------------------- European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0) 1223 492 502 |
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From: Pesce, V. (DDNG) <Val...@fa...> - 2018-02-08 16:56:49
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[On behalf of the RDA Agrisemantics WG] Dear all, you are receiving this email because your email address is registered as a contact email address for a data standard / vocabulary included in the GODAN Action Map of agri-food data standards. We are reaching out to all experts in data standardization in the area of food and agriculture in an effort to gather relevant use cases for the improvement of data standards and vocabularies to make them more usable. The Agrisemantics Working Group of RDA (Research Data Alliance) is collecting input on use cases on the use of semantic resources for agricultural data - be those controlled vocabularies, metadata schemas or ontologies. We are interested in knowing what problems and limitations people face when dealing with them. To this end, we have set up a short survey, 6 questions, that you can find as an online document: https://goo.gl/u9yrzs. Your answers will contribute to the final output of the group - recommendations on tools & services to be included in future infrastructures for open science in agriculture. If you want to participate in the survey with your use case, please do so by Feb 15. To provide your use case: 1. go to the dedicated shared folder: https://goo.gl/XuBwFa 2. make your own copy of the survey and send it to the chairs (see below) In case of doubts, do not hesitate to ask one of the undersigned chairs! Please be informed that all shared folders are public. We also plan on publishing the collected use cases as support material for the requirement document. Many thanks for your support! Kind regards, The Agrisemantics WG chairs Cat...@fa..., sop...@in..., B.W...@ca..., pz...@ag... |
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From: Sirarat S. <si...@eb...> - 2018-01-15 13:41:39
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Dear EFO users, EFO version 2.92 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> -------------------------------------------------------------- |
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From: Sirarat S. <si...@eb...> - 2017-12-18 16:00:47
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Dear EFO users, EFO version 2.91 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... <mailto:efo...@li...> by mid 2018. ================================================ Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> -------------------------------------------------------------- |
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From: Sirarat S. <si...@eb...> - 2017-11-15 15:04:29
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Dear EFO users, There seems to be a censoring issue with messages containing specific keywords that Sourceforge does not seem to like forwarding to our users. If you currently access EFO via Sourceforge and are registered in this mailing list, it is very important that you see our announcement https://sourceforge.net/p/efo/mailman/message/36116399/ <https://sourceforge.net/p/efo/mailman/message/36116399/> . Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> -------------------------------------------------------------- |
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From: Sirarat S. <si...@eb...> - 2017-11-15 14:51:02
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Dear EFO users, EFO version 2.90 is now live and available on the EFO website: https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at our new repository: https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt <https://github.com/EBISPOT/efo/blob/master/ExFactor%20Ontology%20release%20notes.txt> We have updated our repository. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. ==============NEW MAILING LIST================== We will be phasing out our Sourceforge mailing list in order to formalise our communication to an EBI-based mailing list. Please sign up for the new mailing list at: https://listserver.ebi.ac.uk/mailman/listinfo/efo-users <https://listserver.ebi.ac.uk/mailman/listinfo/efo-users> We are projecting to freeze communications via efo...@li... by mid 2018. ================================================ Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> -------------------------------------------------------------- |
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From: Simon J. <ju...@eb...> - 2017-10-27 08:40:59
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Dear Abbas, You can also get the sourcecode for bubastis here if you want to run it locally. https://github.com/EBISPOT/bubastis Cheers Simon > On 26 Oct 2017, at 17:18, Sirarat Sarntivijai <si...@eb...> wrote: > > Dear Abbas, > > Thank you very much for contacting us. If you are looking to track ontology change, we have a new and improved tool - Diachron that lets you track various activities of ontology change (see example by going to www.ebi.ac.uk/ols/ontologies/efo <http://www.ebi.ac.uk/ols/ontologies/efo> and click on “Term history” tab). For API access, please drop a message to ont...@eb... <mailto:ont...@eb...> (copied here), and someone will get back to you. > > Thank you very much, > Sira > > -------------------------------------------------------------- > Sirarat Sarntivijai, PhD > Bioinformatician - Ontologist > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus, > Hinxton, Cambridge, United Kingdom CB10 1SD > > Tel: +44 (0)1223 494 214 > URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> > -------------------------------------------------------------- > >> On 26 Oct 2017, at 17:09, su...@eb... <mailto:su...@eb...> wrote: >> >> >> Hi >> >> Please can you help with this enquiry? >> >> Thanks in advance >> >> Karyn >> >> >> >> >> Delivered-To: rt...@sy... <mailto:rt...@sy...> >> Subject: regarding the bubastis system >> Return-Path: <no...@eb... <mailto:no...@eb...>> >> X-Original-To: rt...@sy... <mailto:rt...@sy...> >> Date: Thu, 26 Oct 2017 16:47:15 +0100 >> Reply-To: ab...@ug... <mailto:ab...@ug...> >> Message-ID: <201...@sm... <mailto:201...@sm...>> >> Content-Type: text/plain; charset="utf-8" >> To: su...@eb... <mailto:su...@eb...> >> From: no...@eb... <mailto:no...@eb...> >> X-RT-Original-Encoding: utf-8 >> X-RT-Interface: Email >> Content-Length: 718 >> >> User's email address: ab...@ug... <mailto:ab...@ug...> >> Feedback topic: General Feedback >> Referrer URL: https://www.ebi.ac.uk/about/contact <https://www.ebi.ac.uk/about/contact> >> User's IP address: 128.192.62.242 >> Web browser used: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.106 Safari/537.36 >> Message sent: Thursday 26 October 2017, 16:47 >> >> Message content: >> ------------------------ >> >> Hi, >> My name is Abbas and I am PhD student at university of georgia, USA. I saw your bubastis system and it seems very interesting. As we might need a system like that to achieve a different application, I was wondering if we can have your system and install it locally, as our ontology located behind firewalls and cannot access from outside. >> >> Bests >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> >> EFO-users mailing list >> EFO...@li... <mailto:EFO...@li...> >> https://lists.sourceforge.net/lists/listinfo/efo-users > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > EFO-users mailing list > EFO...@li... > https://lists.sourceforge.net/lists/listinfo/efo-users |
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From: Sirarat S. <si...@eb...> - 2017-10-26 16:18:39
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Dear Abbas, Thank you very much for contacting us. If you are looking to track ontology change, we have a new and improved tool - Diachron that lets you track various activities of ontology change (see example by going to www.ebi.ac.uk/ols/ontologies/efo <http://www.ebi.ac.uk/ols/ontologies/efo> and click on “Term history” tab). For API access, please drop a message to ont...@eb... <mailto:ont...@eb...> (copied here), and someone will get back to you. Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 URL: https://www.ebi.ac.uk/about/people/sirarat-sarntivijai <https://www.ebi.ac.uk/about/people/sirarat-sarntivijai> -------------------------------------------------------------- > On 26 Oct 2017, at 17:09, su...@eb... wrote: > > > Hi > > Please can you help with this enquiry? > > Thanks in advance > > Karyn > > > > > Delivered-To: rt...@sy... > Subject: regarding the bubastis system > Return-Path: <no...@eb...> > X-Original-To: rt...@sy... > Date: Thu, 26 Oct 2017 16:47:15 +0100 > Reply-To: ab...@ug... > Message-ID: <201...@sm...> > Content-Type: text/plain; charset="utf-8" > To: su...@eb... > From: no...@eb... > X-RT-Original-Encoding: utf-8 > X-RT-Interface: Email > Content-Length: 718 > > User's email address: ab...@ug... > Feedback topic: General Feedback > Referrer URL: https://www.ebi.ac.uk/about/contact > User's IP address: 128.192.62.242 > Web browser used: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.106 Safari/537.36 > Message sent: Thursday 26 October 2017, 16:47 > > Message content: > ------------------------ > > Hi, > My name is Abbas and I am PhD student at university of georgia, USA. I saw your bubastis system and it seems very interesting. As we might need a system like that to achieve a different application, I was wondering if we can have your system and install it locally, as our ontology located behind firewalls and cannot access from outside. > > Bests > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > EFO-users mailing list > EFO...@li... > https://lists.sourceforge.net/lists/listinfo/efo-users |
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From: <su...@eb...> - 2017-10-26 16:09:26
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Hi Please can you help with this enquiry? Thanks in advance Karyn |
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From: Tony B. <tbu...@eb...> - 2017-10-25 11:55:00
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Hi Rachel, I've just been referred your email on your request about EFO disease groupings - thanks for getting in touch. I'm forwarded this email to the efo...@li... list. You can address your question here. Please let me know if I can help further. Thanks, Tony -- Tony Burdett Technical Co-ordinator - Samples, Phenotypes and Ontologies Team, European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: + 44 (0) 1223 494 624 On 25/10/17 11:59, su...@eb... wrote: > Hi > > Rodrigo asked me to forward this query to you both. I'm not sure if you can see > all the history however the original mail is pasted below. Andrew Cowley > advised the user to contact you directly however she hasn't had any response. > > Thanks in advance for dealing with this one. > > Regards > > Karyn > > Subject: question about EFO grouping > Date: Thu, 28 Sep 2017 13:43:26 +0100 > To: su...@eb... > From: no...@eb... > Download (untitled) (https://helpdesk.ebi.ac.uk/Ticket/Attachment/4072754/2576405/) > / with headers (https://helpdesk.ebi.ac.uk/Ticket/Attachment/WithHeaders/2576405) > text/plain 460BUser's email address: rac...@ni... > Feedback topic: EFO > Referrer URL: http://www.ebi.ac.uk/about/contact > User's IP address: 137.187.177.48 > Web browser used: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) > AppleWebKit/603.3.8 (KHTML, like Gecko) Version/10.1.2 Safari/603.3.8 > Message sent: Thursday 28 September 2017, 13:43 > > Message content: > ------------------------ > > Hello: whom do I contact if I feel that a disease is in the wrong EFO group? > Thanks > > |
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From: Sirarat S. <si...@eb...> - 2017-10-24 09:59:59
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Dear EFO users, Our million apologies for spamming your mailbox. There is an upcoming change to our release process. If you currently access EFO via the Sourceforge portal, it is important that you see our announcement at https://sourceforge.net/p/efo/mailman/message/36087205/ <https://sourceforge.net/p/efo/mailman/message/36087205/>. Thank you very much, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 E-mail: si...@eb... <mailto:si...@eb...> -------------------------------------------------------------- |
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From: Dani W. <dw...@eb...> - 2017-10-24 09:25:00
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It seems the notification emails go through for some users and not for others. Apologies if you are getting spammed - we will try to resolve this asap but please bear with us while we figure out what’s going on. Thanks Dani Welter, PhD Ontologist/Bioinformatician Samples, Phenotypes and Ontologies Team --------------------------------------- European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0) 1223 492 502 |
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From: Simon J. <ju...@eb...> - 2017-10-24 08:59:30
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We’ve noticed that e-mails to the efo-users list including the latest EFO release announcement didn’t get through to some people this month. I’m sending this e-mail as a test to see if sourceforge has resolved things. Thanks Simon --------------------------------------------------- Simon Jupp Samples Phenotypes and Ontologies Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Web: http://www.ebi.ac.uk/~jupp <http://www.ebi.ac.uk/~jupp>Tel: + 44 (0) 1223 494 664 |
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From: Sirarat S. <si...@eb...> - 2017-10-23 14:39:19
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Dear EFO users, Last week we released EFO 2.89 and announced our migration to Github beginning in EFO 2.90. This migration will not affect content or structure of EFO. ——In EFO 2.90 (November 2017 release)—— Please read carefully if you currently access EFO files via our Sourceforge portal. EFO development and release versions are moving to GitHub. There are NO critical changes to the content or structure of EFO and the PURL address http://www.ebi.ac.uk/efo/efo.owl <http://www.ebi.ac.uk/efo/efo.owl> <http://www.ebi.ac.uk/efo/efo.owl> <http://www.ebi.ac.uk/efo/efo.owl%3E>; will always resolve to the latest EFO OWL file, so most users should not be affected by this change. Accessing files via the EFO website at https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> <https://www.ebi.ac.uk/efo/> <https://www.ebi.ac.uk/efo/%3E>; will also resolve to the latest release of EFO. Beginning in November 2017 release, EFO 2.90, development snapshots and public releases will be available from our Github repository at https://github.com/EBISPOT/efo <https://github.com/EBISPOT/efo> <https://github.com/EBISPOT/efo> <https://github.com/EBISPOT/efo%3E>;. Detailed information on how to access the files will be spelled out in next months release announcement. We will no longer provide our release documentation in the form of ExFactor Ontology release notes.txt as available from https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt> <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt> <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt%3E>;, but instead will redirect all the change log monitoring to the “Ontology history” tab provided by the Ontology Lookup Service (OLS) https://www.ebi.ac.uk/ols/ontologies/efo <https://www.ebi.ac.uk/ols/ontologies/efo> <https://www.ebi.ac.uk/ols/ontologies/efo> <https://www.ebi.ac.uk/ols/ontologies/efo%3E>;. If you have any questions or concerns on the upcoming changes, please do not hesitate to contact us. Cheers, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 E-mail: si...@eb... <mailto:si...@eb...> -------------------------------------------------------------- |
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From: Sirarat S. <si...@eb...> - 2017-10-16 15:59:59
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Dear EFO users, EFO version 2.89 is now live and available at the EFO website: http://www.ebi.ac.uk/efo/ <http://www.ebi.ac.uk/efo/> This release, we are still business-as-usual from Sourceforge. Please see release notes for a summary and detailed report of changes and modifications at https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt> Reminder that SourceForge has upgraded the EFO project which requires new commands to checkout and commit code. Please see the following links for more information: https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/ <https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/> https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion <https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion> See the release notes for a full list of new terms added. ============= Github migration in EFO 2.90 =============== Please read carefully if you currently access EFO files via our Sourceforge portal. EFO development and release versions are moving to GitHub. There are NO critical changes to the content or structure of EFO and the PURL address http://www.ebi.ac.uk/efo/efo.owl <http://www.ebi.ac.uk/efo/efo.owl> will always resolve to the latest EFO OWL file, so most users should not be affected by this change. Accessing files via the EFO website at https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> will also resolve to the latest release of EFO. Beginning in November 2017 release, EFO 2.90, development snapshots and public releases will be available from our Github repository at https://github.com/EBISPOT/efo <https://github.com/EBISPOT/efo>. Detailed information on how to access the files will be spelled out in next months release announcement. We will no longer provide our release documentation in the form of ExFactor Ontology release notes.txt as available from https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt>, but instead will redirect all the change log monitoring to the “Ontology history” tab provided by the Ontology Lookup Service (OLS) https://www.ebi.ac.uk/ols/ontologies/efo <https://www.ebi.ac.uk/ols/ontologies/efo>. If you have any questions or concerns on the upcoming changes, please do not hesitate to contact us. Keep calm and EFO on. Cheers! Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 E-mail: si...@eb... <mailto:si...@eb...> -------------------------------------------------------------- |
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From: Sirarat S. <si...@eb...> - 2017-10-16 15:27:12
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Dear EFO users, EFO version 2.89 is now live and available at the EFO website: http://www.ebi.ac.uk/efo/ <http://www.ebi.ac.uk/efo/> This release, we are still business-as-usual from Sourceforge. Please see release notes for a summary and detailed report of changes and modifications at https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt> Reminder that SourceForge has upgraded the EFO project which requires new commands to checkout and commit code. Please see the following links for more information: https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/ <https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/> https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion <https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion> See the release notes for a full list of new terms added. ============= Github migration in EFO 2.90 =============== Please read carefully if you currently access EFO files via our Sourceforge portal. EFO development and release versions are moving to GitHub. There are NO critical changes to the content or structure of EFO and the PURL address http://www.ebi.ac.uk/efo/efo.owl <http://www.ebi.ac.uk/efo/efo.owl> will always resolve to the latest EFO OWL file, so most users should not be affected by this change. Accessing files via the EFO website at https://www.ebi.ac.uk/efo/ <https://www.ebi.ac.uk/efo/> will also resolve to the latest release of EFO. Beginning in November 2017 release, EFO 2.90, development snapshots and public releases will be available from our Github repository at https://github.com/EBISPOT/efo <https://github.com/EBISPOT/efo>. Detailed information on how to access the files will be spelled out in next months release announcement. We will no longer provide our release documentation in the form of ExFactor Ontology release notes.txt as available from https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt>, but instead will redirect all the change log monitoring to the “Ontology history” tab provided by the Ontology Lookup Service (OLS) https://www.ebi.ac.uk/ols/ontologies/efo <https://www.ebi.ac.uk/ols/ontologies/efo>. If you have any questions or concerns on the upcoming changes, please do not hesitate to contact us. Keep calm and EFO on. Cheers! Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 E-mail: si...@eb... <mailto:si...@eb...> -------------------------------------------------------------- |
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From: Sparks, R. (NIH/N. [E] <rac...@ni...> - 2017-09-29 15:35:02
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Hello: It is not clear to me why pneumoconiosis (http://www.orpha.net/ORDO/Orphanet_182098) and any of its subclasses is in the infectious disease or bacterial disease group. These are immune reactions to inhaled particulate matter, and not bacterial infections. Could you please clarify this grouping? Thank you, Rachel Rachel Sparks, MD, MPH Clinical Fellow, Allergy and Immunology Systems Genomics and Bioinformatics Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda, Maryland 20892-1899 Desk: 240-292-4642 Pager: 301-496-1211 x 12541 rac...@ni...<mailto:rac...@ni...> The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. |
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From: Sparks, R. (NIH/N. [E] <rac...@ni...> - 2017-09-29 14:48:09
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Hello: It is not clear to me why osteoarthritis (EFO_0002506) is in the autoimmune disease group, as it is not generally considered an autoimmune disease (but rather a degenerative disease). Can somebody please clarify? Thank you, Rachel Rachel Sparks, MD, MPH Clinical Fellow, Allergy and Immunology Systems Genomics and Bioinformatics Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda, Maryland 20892-1899 Desk: 240-292-4642 Pager: 301-496-1211 x 12541 rac...@ni...<mailto:rac...@ni...> The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. |
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From: Sirarat S. <si...@eb...> - 2017-09-18 14:31:09
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Dear EFO users, EFO version 2.88 is now live and available at the EFO website: http://www.ebi.ac.uk/efo/ <http://www.ebi.ac.uk/efo/> Please see release notes for a summary and detailed report of changes and modifications at https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt <https://sourceforge.net/p/efo/code/HEAD/tree/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt> Reminder that SourceForge has upgraded the EFO project which requires new commands to checkout and commit code. Please see the following links for more information: https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/ <https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/> https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion <https://sourceforge.net/apps/trac/sourceforge/wiki/Subversion> See the release notes for a full list of new terms added. Keep warm people!, Sira -------------------------------------------------------------- Sirarat Sarntivijai, PhD Bioinformatician - Ontologist European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom CB10 1SD Tel: +44 (0)1223 494 214 E-mail: si...@eb... <mailto:si...@eb...> -------------------------------------------------------------- |
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