[OTDev] Errors and warnings in datasets
Nina Jeliazkova jeliazkova.nina at gmail.comTue Oct 12 11:18:20 CEST 2010
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Hi Surajit, All, On 12 October 2010 11:54, surajit ray <mr.surajit.ray at gmail.com> wrote: > Hi , > > Would the target of a ot:hasMessage be an object defined in the ontology ? > OR would it be just text literal ? > > I've suggested a literal for the sake of simplicity (and because text is mentioned in the first email from Christoph) , but more complex constructs can be imagined as well. > Just a suggestion ..... > It would be helpful to have an class on the lines of a "logfile" (in > opentox > owl). Coupled with a ot:hasLogreport (on the dataset,data-entry etc) we > could potentially use this construct for various levels of structured log > reports for any task. > Indeed. We'll then need to track which service generates the log report, I imagine there could be multiple ones associated with a data entry, based on processing by different services. @All - Is there any ontology that deals with logging in general ? Best regards, Nina > The log could cover everything from errors,warnings,messages to suggestion > for next steps etc. > > Cheers > Surajit > > On 12 October 2010 13:31, Nina Jeliazkova <jeliazkova.nina at gmail.com> > wrote: > > > 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 do you think? > > > > Nina > > > > > > > > Best regards, > > > Christoph > > > _______________________________________________ > > > Development mailing list > > > Development at opentox.org > > > http://www.opentox.org/mailman/listinfo/development > > > > > _______________________________________________ > > Development mailing list > > Development at opentox.org > > http://www.opentox.org/mailman/listinfo/development > > > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development >
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