Dear "member" of the OpenTox community:

In the OpenTox Association general assembly the importance of the use 
cases was again underpinned by a large group of people and two new use 
cases additionally to the list given below were proposed:

f) Asish, Andreas, Thomas: Data integration approaches for OpenTox
g) Ahmed: Use cases for specific endpoints from generation of data to 
regulation

Two keep the momentum, I propose to have a follow-up virtual meeting in 
the nearest future. I created a doodle pole to find a data and time, 
which is convenient for most people.

http://doodle.com/poll/s32swgt4tdb2ftdd

This will be another joined meeting of all working groups, which will be 
used to identify people interested in specific use cases, which then can 
be discussed in smaller groups. I hope to "see" many of you in this meeting.

Looking forward to active discussion.
Best regards and thank you very much.
Thomas





Thomas Exner schrieb:
> Dear "member" of the OpenTox community:
>
> With great pleasure I am looking back at our OpenTox Euro meeting in
> Dublin. I really think it was a great meeting with many excellent talks
> and productive discussions and I hope that you now see yourself as part
> of OpenTox. My special thanks goes especially to the group participating
> in the working group discussions on the first day. Even if we had some
> virtual meetings before, I see this date as the real staring point of
> the working group activities. What was planned as four separate meetings
> ended up to be one meeting of the complete group since we directly
> recognized that the topics of the four working groups are extremely
> interlinked. There is need for strong interactions with the AOP
> activities leaded by Clemens Wittwehr (WG2) in two directions: 1) Data
> from the OpenTox community should be made available to verify APOs and
> 2) information from AOPs should be included in OpenTox modelling tools.
> This is only possible with standardized data/metadata (WG3, Thomas
> Exner) and extended APIs (WG1, Christoph Helma). All this has then to be
> provided in a user-friendly environment (WG4, Tim Dudgeon). The
> following discussion showed that there are many different opinions and
> demands on interoperability and standards. To get all these into one
> working model is definitely not an easy task. To approach it, two main
> goals for the near future were proposed:
>
> 1) Documenting the past: Unfortunately, the openTox developments are
> very fragmented at the moment. To change that, Tim volunteered to
> generate an overview of existing OpenTox services. You can find more
> details in his E-mail below. Besides the services, which resulted from
> the OpenTox projects and its successors, we are also welcoming all
> suggestions for services, which should be linked to OpenTox. Especially,
> the input from Yanli Wang (PubChem) was extremely helpful in this
> respect and we are looking forward to a fruitful cooperation.
>
> 2) Planning for the future: Even more important than file format
> standards for the data and metadata are quality standards of the data.
> Only if we can judge the quality of the data, we can decide if we want
> to use them in modelling or if it is acceptable for regulatory purposes.
> But already these two applications demand for different information
> stored as metadata. Is it possible to design a infrastructure, which
> stores all data/metadata, so that it can easily be retrieved and
> included in decision making or converted to reports like REACH and SEND?
> To find this out, use cases or better backbones of uses cases will be
> developed and analyses regarding their demands on the data formats. In
> Dublin some more volunteers were identified:
> a) Clements: Data for regulatory purposes
> b) Christoph, Thomas: Datasets for tox prediction
> c) Thomas, Joh Dokler (Douglas Connect) (and Yanli Wang): Data exchange
> using PubChem as most important example
> d) Roland Grafström, Hristo Alajdov, Clements, Thomas: Interacting and
> modelwith AOPs
> e) Ignacio Gonzalez Suarez (PMI): standards for high contents screening
> Maurice Whelan (EC) pointed us to the successful use of use cases in the
> SEURAT-1 program including ToxBank and ask us to take a look at them,
> which we definitely will. To cover even more opinions, IO would like t
> ask you to propose additional use cases. These don't have to be fancy
> but just describe your daily life --> How do you use tox related data
> and what information you need or would like to see associated with this
> data. Just a short draft of the work flow is enough highlighting the
> problems in current datasets. I will create a doodle (additional
> invitation will follow soon) to find a date for a follow-up virtual
> meeting end of this month in which the use cases can be discussed.
>
> Thanks again for all the valuable input on the working groups.
> Thomas
>
>
> ______________________________________________________________________
> Tim Dudgeon:
>
> Hi All,
>
> Here are some thoughts on what we can do to create a useful directory of
> OpenTox services.
> I'd welcome feedback on this.
>
> 1. List of services
> See first sheet here:
> https://docs.google.com/spreadsheets/d/13RlxLQWunwJAvvjPQWDSciokUnZQhz0vCQyMyBt4jNI/edit#gid=0
>
> Whilst a useful start, its probably not that useful at present.
> It would benefit from a more complete description of each service,
> including a description of the methodology behind the prediction
> services, and other aspects that differentiate the services.
> And maybe some other columns could be useful (please suggest).
>
> 2. List of models
> A service on its own isn't much use to a user. Its presumably the
> ability to use a model within a service to generate predictions that's
> of real use. Therefore it would be useful to somehow catalog the
> available models in each service. But new models can be created on the
> fly, and just because a user has created a model doesn't mean its any
> use, so maintaining a useful catalog for this across all services would
> be almost impossible.
> But maybe we can handle this if we treat this on the basis of "approved"
> models, which have been generated from "approved" datasets (see next
> section) and have been "validated" (in the sense of having been shown to
> generate reasonable results).
> Do you think this is possible/reasonable to try to achieve?
>
> 3. List of datasets
> If predictions are to be comparable between different services then they
> need to be based on the same datasets.
> Therefore it might be useful to prepare a list of "approved" datasets
> that can be use to make models, and to have those datasets available in
> standard formats.
> This way each service could generate predictive models using these
> "standard" datasets, and this can allow different models to be compared.
> These could form the core of the "List of models" described above.
> These standard datasets would not be restricted to those within OpenTox,
> but would include ones from ToxCast, Tox21 and other places.
> Do you think this is possible/reasonable to try to achieve?
>
>
> I welcome any thoughts on any of this.
>
> Tim
>
>
>

_______________________________________________
Alllists mailing list
Alllists at opentox.org
http://www.opentox.org/mailman/listinfo/alllists