OpenTox Working Groups
One of the main goals of the OpenTox community to provide sustainable availability and integration of data resources into practical work situations of scientists, risk assessors, managers and regulators was addressed by establishing working groups. These will further develop standards and software and will enable and educate a growing community of application developers. If you are interested in participating in these activities, please contact email@example.com.
Four groups have been set up until now:
WG 1: Application Programming Interfaces (APIs), Chair: Christoph Helma (in silico toxicology)
WG 2: Adverse Outcome Pathways (AOPs), Chair: Clemens Wittwehr (EC JRC)
WG 3: Data Standards, Chair: Thomas Exner (DC)
WG 4: Deployment, Chair: Tim Dudgeon (Informatics Matters)
The progress of these groups are discussed in regular face-to-face and virtual meetings. Whenever possible they are integrated in and arranged around OpenTox conferences and workshops.
1. Joint VM of working group 1 and 4 (11 Sep. 2015) à minutes (WG1+4_VM_20150911.pdf)
2. Joint VM of working group 2 and 3 (11 Sep. 2015) à minutes (WG2+3_VM_20150911.pdf)
3. Working group day at the OpenTox Euro 2015 (30 Sep. 2015) à minutes (WG_OpenToxEuro_20150930.pdf)
4. Joint VM of working groups 1-4 (12 Nov. 2015) à minutes (WG_VM_20151112.pdf)
5. Working group week at OpenTox Basel (29 Feb to 3 March 2016) à program
6. Working group activities at OpenTox USA (11-12 Apr. 2016) à program
Additionally, working groups over arching topics have been formulated as case studies, which will help to IDENTIFY challenges and to develop approaches and workflows to overcome these.
- 1. Data for specific endpoints from generation to regulation: This subgroup will protocol the data flow for two specific endpoints: transcriptomics and high contents imaging/analysis. The first workflow is relatively well-established and the needed steps are more or less known. Nevertheless, there currently is no accepted automatic protocol and the manual steps performed are time-consuming, error-prone and sometimes not reproducible and, thus, not fit for regulatory purposes. The second workflow is even more complicated, since here not even the data/metadata, which has to be shared is well defined as highlighted by Ignacio Gonzalez Suarez in his talk at OpenTox Euro 2015 in Dublin.
- 2. Data for modelling and data integration: (Minimal) data/metadata quality standards will be defined for modelling, since trustworthy models can only be developed on the basis of retraceable/reproducible data. The second task will then be to incorporate additional data sources. Prioritization of these will include considering the quality standards. One of the most important sources is PubChem.
- 3. Regulatory reporting (link to OpenTox WG2 Case Studies v1.pdf): Even if this is already partly covered by the first topic, the specific demands of regulatory reports justify an additional subgroup on this topic. Main question to be answered here is how to prepare and handle data so that it can be directly used for reporting in the different formats (REACH, SEND, OCED harmonized templates, …).
- 4. Immense amounts of information are collected in adverse outcome pathways. To help their developments (link to AOP-XML project proposal Final.pdf) but also to use this information in modelling, interfaces between OpenTox databases/services and the AOP knowledge base as the central source for validated AOPs as well as AOPs under development are needed.