From barry.hardy at douglasconnect.com Thu Jul 30 10:54:44 2015 From: barry.hardy at douglasconnect.com (Barry Hardy) Date: Thu, 30 Jul 2015 10:54:44 +0200 Subject: [OpenTox Ontology] OpenTox Euro 2015 - abstract submission deadline for talk Message-ID: <55B9E654.90002@douglasconnect.com> Reminder - the abstract submission deadline for a talk at the OpenTox Euro 2015 meeting in Ireland is this week (Friday 31 July). http://www.opentox.net/submit-abstract-poster-or-chair We will continue accepting for posters. Barry The OpenTox Euro 2015 meeting takes place 30 Sept - 2 Oct in Dublin, Ireland. The conference theme is Reproducible High Quality Safety Science on Complex Systems and will include conference sessions on Information Requirements & Standards, Characterisation of Systems, High Content Screening, Metabolism, Modelling Cellular Perturbations & Responses, Linking Parameters & Evidence across Scales, Simulation, Systems Biology and Knowledge Integration Supporting Decision Making. OpenTox Association Working group meetings will be held on the topics of Application Programming Interfaces, Adverse Outcome Pathways, Data and Metadata Standards and Resource Deployment. The meeting will also include a General Assembly of the Association in addition to hands-on modelling and analysis sessions, poster session and knowledge cafes. To submit an abstract for the meeting: (Deadlines: 31 July for speaker program, 31 August for posters) http://www.opentox.net/submit-abstract-poster-or-chair Information and updates on the program will be posted at: http://www.opentox.net/events/opentox-euro-2015 best regards Barry Hardy President, OpenTox Association On behalf of the Organising Committee On the OpenTox Association Following up on the initial OpenTox project which was funded by the EU under FP7, OpenTox has developed as an open standards platform supporting application and infrastructure development in predictive toxicology and safety assessment. The OpenTox Association was founded 27 March this year as an international member-based non-profit association. The purpose of the Association is to promote the community-based exchange and use of open knowledge, software, methods, tools, data, reference resources, and standards in the scientific activities of predictive toxicology, safety assessment and risk management, including the 3Rs goal of the Reduction, Refinement and Replacement of Animal Testing. More information on the Association: http://www.opentox.net/the-opentox-association From thomas.exner at uni-tuebingen.de Thu Jul 30 17:00:10 2015 From: thomas.exner at uni-tuebingen.de (Thomas Exner) Date: Thu, 30 Jul 2015 17:00:10 +0200 Subject: [OpenTox Ontology] OpenTox Working Group Data Standards and Metadata Message-ID: <55BA3BFA.9050901@uni-tuebingen.de> Dear all: As part of the activities of the OpenTox Association, working groups on different aspects of OpenTox have been launched. As leader of the working group on data standards and metadata, I would like to invite everyone to participate in our activities. The goals of the group are described below and will also be presented and discussed on the OpenTox Euro meeting in Dublin (Sep. 30 - Oct. 2). If you are interested or have any question, please do not hesitate to contact me. Best regards. Thomas WG3 Defining Standards for Data and Metadata in OpenTox Large amounts of toxicity data is generated worldwide on a daily basis and stored in different open and inhouse databases. The format of the data and the availability of metadata, describing the experimental setups and in this way the quality of the data, differ strongly prohibiting analysis combining data from different resources. The Data Standards working group will develop standards for data file of toxicity related endpoints as well as approaches to document the related metadata in human- but especially also computer-readable form. These will consider achievements from earlier and on-going projects like ToxBank and eNanoMapper but also the requirements imposed by regulatory formats like REACH and SAND. To achieve this, the working group plans to: 1. generate an on-line catalog of available data resources and review the data formats used. 2. consolidate the available formats and define recommendations. 3. communicate with experts to understand the specific requirements of each experimental technique. 4. discuss possibilities of harmonization with vendors of experimental equipment. -- ________________________________________________________________________________ PD Dr. Thomas E. Exner Theoretische Pharmazeutische Chemie & Biophysik Lehrstuhl Pharmazeutische Chemie Pharmazeutisches Institut Eberhard Karls Universit?t T?bingen Auf der Morgenstelle 8 (Haus B) 72076 T?bingen Germany Tel.: +49-(0)7071-2976969 Mobil: +49-(0)171-3807485 Fax: +49-(0)7071-295637 E-Mail: Thomas.Exner[at]uni-tuebingen.de Fachbereich Chemie und Zukunftskolleg Universit?t Konstanz 78457 Konstanz Germany Tel.: +49-(0)7531-882015 Fax: +49-(0)7531-883587 E-Mail: Thomas.Exner[at]uni-konstanz.de ________________________________________________________________________________ From jsluka at indiana.edu Thu Jul 30 18:42:20 2015 From: jsluka at indiana.edu (Sluka, James Patrick) Date: Thu, 30 Jul 2015 16:42:20 +0000 Subject: [OpenTox Ontology] OpenTox Working Group Data Standards and Metadata In-Reply-To: <55BA3BFA.9050901@uni-tuebingen.de> References: <55BA3BFA.9050901@uni-tuebingen.de> Message-ID: Thomas This is a great start. I would add one more bullet point; 5. Explore harmonization with other biological and biomedical domains for standards for data and metadata. It seems to me that we do not want to develop standards for all the various types of assays that might be done as tox studies; microarray, tissue culture, model animal in vivo, histology, etc. Instead we want those "technique domains" to develop their own data and annotation standards that best fits their data and experimental characteristics. What we really need are methods of controlling how the toxicological information (data and meta-data) is append to the domain-specific formats. This seems to me to be two issues; (1) prodding (coercing, begging) the domain-specific communities to develop a standard for their domains that is compatible with annotation using toxicological concepts and (2) developing a controlled vocabulary and/or ontology suitable for that annotation. Jim Sluka Biocomplexity Institute Indiana University -----Original Message----- From: ontology-bounces at opentox.org [mailto:ontology-bounces at opentox.org] On Behalf Of Thomas Exner Sent: Thursday, July 30, 2015 11:00 AM To: ontology at opentox.org Subject: [OpenTox Ontology] OpenTox Working Group Data Standards and Metadata Dear all: As part of the activities of the OpenTox Association, working groups on different aspects of OpenTox have been launched. As leader of the working group on data standards and metadata, I would like to invite everyone to participate in our activities. The goals of the group are described below and will also be presented and discussed on the OpenTox Euro meeting in Dublin (Sep. 30 - Oct. 2). If you are interested or have any question, please do not hesitate to contact me. Best regards. Thomas WG3 Defining Standards for Data and Metadata in OpenTox Large amounts of toxicity data is generated worldwide on a daily basis and stored in different open and inhouse databases. The format of the data and the availability of metadata, describing the experimental setups and in this way the quality of the data, differ strongly prohibiting analysis combining data from different resources. The Data Standards working group will develop standards for data file of toxicity related endpoints as well as approaches to document the related metadata in human- but especially also computer-readable form. These will consider achievements from earlier and on-going projects like ToxBank and eNanoMapper but also the requirements imposed by regulatory formats like REACH and SAND. To achieve this, the working group plans to: 1. generate an on-line catalog of available data resources and review the data formats used. 2. consolidate the available formats and define recommendations. 3. communicate with experts to understand the specific requirements of each experimental technique. 4. discuss possibilities of harmonization with vendors of experimental equipment. -- ________________________________________________________________________________ PD Dr. Thomas E. Exner Theoretische Pharmazeutische Chemie & Biophysik Lehrstuhl Pharmazeutische Chemie Pharmazeutisches Institut Eberhard Karls Universit?t T?bingen Auf der Morgenstelle 8 (Haus B) 72076 T?bingen Germany Tel.: +49-(0)7071-2976969 Mobil: +49-(0)171-3807485 Fax: +49-(0)7071-295637 E-Mail: Thomas.Exner[at]uni-tuebingen.de Fachbereich Chemie und Zukunftskolleg Universit?t Konstanz 78457 Konstanz Germany Tel.: +49-(0)7531-882015 Fax: +49-(0)7531-883587 E-Mail: Thomas.Exner[at]uni-konstanz.de ________________________________________________________________________________ _______________________________________________ Ontology mailing list Ontology at opentox.org http://www.opentox.org/mailman/listinfo/ontology From thomas.exner at douglasconnect.com Mon Aug 17 15:53:29 2015 From: thomas.exner at douglasconnect.com (Thomas Exner) Date: Mon, 17 Aug 2015 15:53:29 +0200 Subject: [OpenTox Ontology] OpenTox Euro 2015 meeting 30 Sept - 2 Oct in Dublin Message-ID: <55D1E759.6000103@douglasconnect.com> Dear all: This is just a short reminder that the deadline for submitting poster abstracts to the OpenTox Euro meeting is 31 August. Additionally, in the name of all OpenTox working group leaders, I would like to invite you to participate in the discussions on the first morning of the conference (30 Sept). If you are not able to attend the conference but are still interested in the working group activities, please contact me for details how to participate virtually. Best regards. Thomas The OpenTox Euro 2015 meeting takes place 30 Sept - 2 Oct in Dublin, Ireland. The conference theme is Reproducible High Quality Safety Science on Complex Systems and will include conference sessions on Information Requirements & Standards, Characterisation of Systems, High Content Screening, Metabolism, Modelling Cellular Perturbations & Responses, Linking Parameters & Evidence across Scales, Simulation, Systems Biology and Knowledge Integration Supporting Decision Making. OpenTox Association Working group meetings will be held on the topics of Application Programming Interfaces, Adverse Outcome Pathways, Data and Metadata Standards and Resource Deployment. The meeting will also include a General Assembly of the Association in addition to hands-on modelling and analysis sessions, poster session and knowledge cafes. To submit an abstract for the meeting: (Deadlines: 31 July for speaker program, 31 August for posters) http://www.opentox.net/submit-abstract-poster-or-chair Information and updates on the program will be posted at: http://www.opentox.net/events/opentox-euro-2015 best regards Barry Hardy President, OpenTox Association On behalf of the Organising Committee From thomas.exner at douglasconnect.com Fri Sep 11 14:42:02 2015 From: thomas.exner at douglasconnect.com (Thomas Exner) Date: Fri, 11 Sep 2015 14:42:02 +0200 Subject: [OpenTox Ontology] Program of OpenTox Euro 2015 online Message-ID: <55F2CC1A.1000806@douglasconnect.com> OpenTox Euro 2015 Conference Program Enabling and Strengthening Reproducible High Quality Safety Science on Complex Systems 30 September to 2 October 2015 University College Dublin The final program is now available at http://www.opentox.net/events/opentox-euro-2015/program Within the general theme of ?Reproducible High Quality Safety Science on Complex Systems?, conference sessions will include ?Information Requirements & Standards?, ?Characterisation of Systems?, ?High Content Screening?, ?Metabolism?, ?Modelling Cellular Perturbations & Responses?, ?Linking Parameters & Evidence across Scales? and ?Knowledge Integration Supporting Decision Making?. Additionally, there will be discussion meetings of the newly established OpenTox working groups. For more information please visit http://www.opentox.net/opentox-euro-2015-sessions/working-groups. Virtual participation in these discussion is possible. Please contact thomas.exner at douglasconnect.com for login details. And please note:Submission of poster abstracts is still open. The poster session will take place on Thursday evening. Poster prizes sponsored by the Irish Society of Toxicology will be awarded and presented to the winners at the final session on Friday. From thomas.exner at douglasconnect.com Fri Sep 11 21:31:28 2015 From: thomas.exner at douglasconnect.com (Thomas Exner) Date: Fri, 11 Sep 2015 21:31:28 +0200 Subject: [OpenTox Ontology] Working Group Virtual Meetings In-Reply-To: <55E6EB2F.6030805@douglasconnect.com> References: <55D44363.60602@douglasconnect.com> <55E42EC7.2020904@douglasconnect.com> <55E6EA13.6040608@douglasconnect.com> <55E6EB2F.6030805@douglasconnect.com> Message-ID: <55F32C10.8000207@douglasconnect.com> Dear all: Please find attached a summary of the pre-conference virtual meetings of Working Group 2 (AOPs) and 3 (standards). If you have addition points for the Dublin meeting, we are happy to include them. Best. Thomas Short presentations: ? Overview of AOP-KB and its modules (Clemens) ? Overview of OpenTox standards and deliverables (Thomas?) ? Data format of AOP-KB Hub (i.e. the upcoming data interchange interface with AOP-KB ? to be handled by Hristo Aladjov, who will be present in the session) ? Intermediate effects DB (IEDB) module, data format "OECD Harmonised Templates": Making science findings acceptable in the regulatory domain (Clemens) Target outcome of discussion (in parentheses the WG(s) that contribute mostly or profit mostly from the outcome) ? Agreement on possible collaboration/synergy between Opentox and AOP-(KB) community, esp. consolidation of available formats and definition of recommendations (both WGs) ? Agreement on joint effort to create a closed vocabulary/ontology in the AOP domain, with a pilot exercise for the "Key Event" naming (mostly WG2) ? Regulatory acceptance of AOPs: How can our collaboration help? (mostly WG2) ? AOP -> consists of several Key Events -> each of them detectable/measurable with one or more test methods: How can our collaboration lead to a homogenous description of methods? (WG2 + WG3) ? More general: How can we define standards for data and metadata exchange (WG2 and WG3) ? Communication strategy with experts to understand the specific requirements of each experimental technique (WG3) ? Possible ways of harmonization with vendors of experimental equipment (WG3) ? Agreement on how to harmonize with other biological and biomedical domains for standards for data and metadata (WG3) ? Linking data and metadata to AOPs produced from them (standard format) (WG2 and WG3) ? Guidance on how to access AOP-KB data for further analysis and predictions in third party systems (WG2 and WG3) Thomas Exner schrieb: > Hi all: > > Please find below the login information for the virtual meetings: > OpenTox > > Please join my meeting from your computer, tablet or smartphone. > https://global.gotomeeting.com/join/715561590 > Password: OpenToxWG > > > You can also dial in using your phone. > United States : +1 (914) 339-0034 > > > Access Code: 715-561-590 > > More phone numbers > Australia : +61 2 6108 4655 > Austria : +43 (0) 7 2088 1403 > Belgium : +32 (0) 28 08 4294 > Canada : +1 (416) 800-9295 > Denmark : +45 (0) 69 91 88 65 > Finland : +358 (0) 942 41 5781 > France : +33 (0) 182 880 459 > Germany : +49 (0) 898 7806 6468 > Italy : +39 0 699 36 98 81 > Netherlands : +31 (0) 208 080 382 > Spain : +34 931 81 6669 > Sweden : +46 (0) 852 503 499 > Switzerland : +41 (0) 435 0167 09 > United Kingdom : +44 (0) 20 3535 0610 > > > > > Thomas Exner schrieb: >> Dear participants of OpenTox Euro: >> >> We have now scheduled the pre-conference virtual meetings to start the >> working group activities. They will take place >> >> Wed. Sep. 9, 3pm CEST for WG2 and WG3 >> Wed. Sep. 9, 4pm CEST for WG1 and WG4 >> >> Please note that we start the working groups completely from scratch. >> Therefore, contributions of people not yet associated with OpenTox are >> highly appreciated. We are looking for people interested in providing >> new services using OpenTox standards and especially experimentalists >> sharing their views on how to best organize data and make them >> accessible in the most useful way. >> >> Best regards. >> Thomas >> >> >> >> >> Thomas Exner schrieb: >>> Dear participants of OpenTox Euro: >>> >>> This is a reminder that the introduction virtual meetings on the opentox >>> working groups will be held next week. Please register for them by going >>> to the doodles given below. >>> >>> Thank you very much. >>> Thomas >>> >>> >>> Thomas Exner schrieb: >>>> Dear participants of OpenTox Euro 2015: >>>> >>>> One topic of the conference will be the future activities of the >>>> OpenTox >>>> working groups on APIs (WG1), AOPs (WG2), Standards (WG3), and >>>> Deployment (WG4) To get a head start, we will organize virtual meetings >>>> previous to the conference. These meetings will be used for a general >>>> introduction and for planning the working group sessions on Wed. Sept. >>>> 30. I set up two doodles to find the best dates for these meetings. >>>> Please put in your availabilities for >>>> >>>> WG1 and WG4 at http://doodle.com/8p2umzuwvte3z8a2 >>>> and for WG2 and WG3 at http://doodle.com/95ywzf8n2y7f27ry >>>> >>>> If you cannot participate at the virtual meetings but still be >>>> interested in the activities of the groups, please contact me so that I >>>> can send you a summary of the discussions. >>>> >>>> Best regards. >>>> Thomas >>>> >>> >> > From thomas.exner at douglasconnect.com Fri Sep 11 21:43:26 2015 From: thomas.exner at douglasconnect.com (Thomas Exner) Date: Fri, 11 Sep 2015 21:43:26 +0200 Subject: [OpenTox Ontology] Working Group Virtual Meetings In-Reply-To: <55F32C10.8000207@douglasconnect.com> References: <55D44363.60602@douglasconnect.com> <55E42EC7.2020904@douglasconnect.com> <55E6EA13.6040608@douglasconnect.com> <55E6EB2F.6030805@douglasconnect.com> <55F32C10.8000207@douglasconnect.com> Message-ID: <55F32EDE.3060802@douglasconnect.com> Dear all: And here the summary for working group 1 (APIs) and 4 (deployment). Looking forward to see as many as possible of you in Dublin. Thomas Joint meeting of WG1 + WG4 on 9-SEP-2015 WG1 related aspects: Discussion will be held in Dublin to condition the APIs towards large data sets . Use of RDF not favoured now, probably will be replaced with JSON Main emphasis needs to be on the data structures, what is provided and not how it is provided. Technical implementation will be guided by the needs of interchangeable data formats. Incorporation of experience from other projects like ToxBank and eNanoMapper, others have to be identified WG4 related aspects: Goals and activities in the Working group overview were agreed. A shared google sheet was set up to create an initial directory of OpenTox services and data (see here). Everyone is encouraged to fill in relevant information. A better solution would be desirable in the longer term that facilitated ensuring the information was kept up to date (e.g. checking if the service is still running, and stating when the code repository was last updated). We do not yet have participants from two of the original OpenTox developers: Nina Keliazkova?s and Stefan Kramer?s groups. Including their expertise in the working group activities is highly desired. Yanli Wang from PubChem attended and pointed out the resources at PubChem. We will want to discuss whether/how to access non-OpenTox compliant services like these. During the Dublin meeting we will initially combine the working groups, and break out into separate groups as necessary. > Thomas Exner schrieb: >> Hi all: >> >> Please find below the login information for the virtual meetings: >> OpenTox >> >> Please join my meeting from your computer, tablet or smartphone. >> https://global.gotomeeting.com/join/715561590 >> Password: OpenToxWG >> >> >> You can also dial in using your phone. >> United States : +1 (914) 339-0034 >> >> >> Access Code: 715-561-590 >> >> More phone numbers >> Australia : +61 2 6108 4655 >> Austria : +43 (0) 7 2088 1403 >> Belgium : +32 (0) 28 08 4294 >> Canada : +1 (416) 800-9295 >> Denmark : +45 (0) 69 91 88 65 >> Finland : +358 (0) 942 41 5781 >> France : +33 (0) 182 880 459 >> Germany : +49 (0) 898 7806 6468 >> Italy : +39 0 699 36 98 81 >> Netherlands : +31 (0) 208 080 382 >> Spain : +34 931 81 6669 >> Sweden : +46 (0) 852 503 499 >> Switzerland : +41 (0) 435 0167 09 >> United Kingdom : +44 (0) 20 3535 0610 >> >> >> >> >> Thomas Exner schrieb: >>> Dear participants of OpenTox Euro: >>> >>> We have now scheduled the pre-conference virtual meetings to start the >>> working group activities. They will take place >>> >>> Wed. Sep. 9, 3pm CEST for WG2 and WG3 >>> Wed. Sep. 9, 4pm CEST for WG1 and WG4 >>> >>> Please note that we start the working groups completely from scratch. >>> Therefore, contributions of people not yet associated with OpenTox are >>> highly appreciated. We are looking for people interested in providing >>> new services using OpenTox standards and especially experimentalists >>> sharing their views on how to best organize data and make them >>> accessible in the most useful way. >>> >>> Best regards. >>> Thomas >>> >>> >>> >>> >>> Thomas Exner schrieb: >>>> Dear participants of OpenTox Euro: >>>> >>>> This is a reminder that the introduction virtual meetings on the >>>> opentox >>>> working groups will be held next week. Please register for them by >>>> going >>>> to the doodles given below. >>>> >>>> Thank you very much. >>>> Thomas >>>> >>>> >>>> Thomas Exner schrieb: >>>>> Dear participants of OpenTox Euro 2015: >>>>> >>>>> One topic of the conference will be the future activities of the >>>>> OpenTox >>>>> working groups on APIs (WG1), AOPs (WG2), Standards (WG3), and >>>>> Deployment (WG4) To get a head start, we will organize virtual >>>>> meetings >>>>> previous to the conference. These meetings will be used for a general >>>>> introduction and for planning the working group sessions on Wed. Sept. >>>>> 30. I set up two doodles to find the best dates for these meetings. >>>>> Please put in your availabilities for >>>>> >>>>> WG1 and WG4 at http://doodle.com/8p2umzuwvte3z8a2 >>>>> and for WG2 and WG3 at http://doodle.com/95ywzf8n2y7f27ry >>>>> >>>>> If you cannot participate at the virtual meetings but still be >>>>> interested in the activities of the groups, please contact me so >>>>> that I >>>>> can send you a summary of the discussions. >>>>> >>>>> Best regards. >>>>> Thomas >>>>> >>>> >>> >> > -------------- next part -------------- A non-text attachment was scrubbed... Name: 150731OpenToxWG4DeploymentOverview.docx.pdf Type: application/x-download Size: 79889 bytes Desc: not available URL: From barry.hardy at douglasconnect.com Fri Oct 16 12:27:07 2015 From: barry.hardy at douglasconnect.com (Barry Hardy) Date: Fri, 16 Oct 2015 12:27:07 +0200 Subject: [OpenTox Ontology] ToxBank Public Forum Message-ID: <5620D0FB.3030009@douglasconnect.com> Dear All: We have an excellent forum program planned for 26,27 October in London. It will be a chance to hear about and discuss the leading progress in the alternative testing field as advanced over the past five years on SEURAT, ToxBank and related projects, and to get a preview of the next exciting chapters going forward in the OpenTox and ToxBank stories. Do come join us if you can - you just have to complete a (free) registration and get to the Wellcome Collection from lunchtime Monday 26 October. (For those unable to make it, we plan to subsequently make a virtual proceedings available.) For full program information download the brochure from: http://www.toxbank.net/ToxBank-PublicForum-brochure_page-by-page.pdf or http://www.toxbank.net/ToxBank-PublicForum-brochure_spreads.pdf best regards Barry Barry Hardy PhD Managing Director Douglas Connect GmbH Baermeggenweg 14 4314 Zeiningen Switzerland