[OTDev] Definition of prediction results
Nina Jeliazkova jeliazkova.nina at gmail.comWed Aug 3 10:23:02 CEST 2011
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Hi Ola, On 3 August 2011 10:58, Ola Spjuth <ola.spjuth at farmbio.uu.se> wrote: > Hi, > > I was wondering if there is a definition how results from predictions are > to be structured in order for clients to interpret it. Yes, all should follow ot:Dataset RDF format in opentox API ontology. http://opentox.org/api/1.1/opentox.owl N3 Example: [] a ot:Dataset ; ot:dataEntry [ a ot:DataEntry ; ot:compound < http://apps.ideaconsult.net:8080/ambit2/compound/100/conformer/143935> ; ot:values [ a ot:FeatureValue ; ot:feature < http://apps.ideaconsult.net:8080/ambit2/feature/27457> ; ot:value "10.335800170898438"^^xsd:double ] ] . <http://apps.ideaconsult.net:8080/ambit2/compound/100/conformer/143935> a ot:Compound . ot:NumericFeature a owl:Class ; rdfs:subClassOf ot:Feature . Where ot:DataEntry is roughly analogous to a row in a spreadsheet , and ot:Feature - to a spreadsheet column, ot:FeatureValue - to a spreadsheet cell. This had been explained in various reports & publications, as well as on opentox site. (Yes, the documentation could be improved :) > For example, if a result has a predicted toxicity value (e.g. Double) All these are represented as ot:Feature, and values i as ot:FeatureValue entries, as in the above example. The feature should be instance of any of ot:NumericFeature, ot:StringFeature , ot:NominalFeature > with accuracy (Double) The feature should be instance of ot:ModelConfidenceFeature and links to the feature with predicted value via ot:confidenceOf property. This is used by the validation service. > and a subtructure (set of atoms), Apart from agreeing to use additional ot:smarts property for structure features , this was not standardised further. > how this is defined for clients to reason and visualize it. I now see HTML > code in some prediction results, and I'm sure this cannot be the intention. > No, it is not :) Nina [1] http://www.jcheminf.com/content/3/1/18 > > Cheers, > > /Ola > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development >
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