On 12 October 2010 14:37, Christoph Helma <helma at in-silico.ch> wrote:

> Excerpts from Nina Jeliazkova's message of Tue Oct 12 10:01:33 +0200 2010:
> > Christoph,
> >
> > On 12 October 2010 10:20, Christoph Helma <helma at in-silico.ch> wrote:
> >
> > > Excerpts from Nina Jeliazkova's message of Mon Oct 11 19:44:01 +0200
> 2010:
> > > > On 11 October 2010 19:51, Christoph Helma <helma at in-silico.ch>
> wrote:
> > > >
> > > > > Excerpts from Nina Jeliazkova's message of Mon Oct 11 17:27:14
> +0200
> > > 2010:
> > > > > > Christoph,
> > > > > >
> > > > > > Could you tell what kind of errors (parsing of SMILES ?) would
> you
> > > like
> > > > > to
> > > > > > store into metadata?  Is it possible to provide examples?
> > > > >
> > > > > It will be a mixed bag of SMILES errors, duplicated structures,
> > > > > incorrect activity entries, .... Examples can be found e.g. at
> > > > > http://toxcreate.org/models under "Warnings:  show".  Simple
> string
> > > > > annotation for concatenated error/warning messages could be
> sufficient.
> > > > >
> > > >
> > > > Ah, ok - agree such information would be very useful.
> > > >
> > > > What do you think about storing these somehow linked to the compounds
> ?
> > >  As
> > > > a start could be simple string annotation , but linked to the
> compounds
> > > and
> > > > not datasets.   Thus one should be able to point to the exact
> compound
> > > where
> > > > the error is.
> > > >
> > > > Perhaps introduce "metadata" for compounds as well?
> > > >
> > >
> > > I think parsing errors are dataset related, not properties of
> > > compounds
> >
> >
> > Well, if it is a SMILES parsing error , I would say it is compound
> related
> >
> > > - and I am reporting also parsing errors for feature values
> > > and formatting errors which are not compound related.
> > >
> >
> > OK.  Then we need metadata/errors for features as well.
> >
> > > Maybe metadata for data entries would be more consistent, but I fear
> > > that could make things too complicated/slow (take e.g. the display of
> > > dataset summaries: it would require to iterate over all dataset entries
> > > just to show error messages - obtaining them directly from dataset
> > > metadata would be far more efficient).
> > >
> >
> > I see. But if one needs to show an error for specific data entry, then
> the
> > client/user is on its own.   For a dataset with more than few errors it
> > might not be easy task.
> >
> > It seems like we need a compromise - errors on both dataset level and
> > dataset entry /compound level . It could be a summary on the dataset
> level
> > for quick display and at the dataset entry /compound or feature level
> > (optional?) if details for specific entry is needed.
> >
> > In this line of thinking,  does it make sense to assign a generic
> container
> > for errors/warnings to every OpenTox object . It could be applicable for
> > models as well (e.g. warning: "default parameters used to derive this
> model"
> > ).
> >
> > Then  the client code will choose what to use based on its preferences /
> > information available.
> >
> > We'll need to add a single property to opentox.owl :
> >
> > <ot> ot:hasMessage/Errors/Warning/find-the-best-word  <Literal>.
>
> What about ot:Info/Warning/Error for each OpenTox object?
>
> ot:Info: informative messages, eg. about default parameters used
> ot:Warning: informative messages about inconsistencies, potential errors..
> (e.g. duplicated measurements)
> ot:Error: Errors, e.g. syntactically incorrect compound structures
>

Fine for me  - should we stick to literals or go for more complex constructs
?

BTW, in opentox.owl there should already be objects of type ot:Error, as
defined in the errors proposal by NTUA.

Also, API - wise ,  how these should be accessed ?  I can think of two
options:

1) via /object/id/metadata   , then we need to invent metadata resources for
objects other than datasets;
2)  via specific links /object/{id}/info , /object/{id}/warning ,
/object/{id}/error


Best regards,
Nina


>
> Best regards,
> Christoph
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