Dear Dimitry, all,

You can find my representation for the first 10 substructures in your
example in the attachment (rdf/xml and turtle formats).

I have noticed that some of your features are not valid smarts (e.g.
CHHHN, CHHCC) and suspect that some brackets around explicit hydrogens
are misssing.

Best regards,
Christoph


Excerpts from Nina Jeliazkova's message of Mon Dec 13 11:36:54 +0100 2010:
> Christoph,
> 
> Here is the example
> 
> <?xml version="1.0" ?><rdf:RDF xmlns:ot="http://www.opentox.org/api/1.1#"
> xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="
> http://www.w3.org/2002/07/owl#"
> xmlns:dc="http://purl.org/dc/elements/1.1/"><owl:Class
> rdf:about="http://www.opentox.org/api/1.1#Dataset"></owl:Class><owl:Class
> rdf:about="http://www.opentox.org/api/1.1#DataEntry"></owl:Class><owl:Class
> rdf:about="http://www.opentox.org/api/1.1#Feature"></owl:Class><owl:Class
> rdf:about="http://www.opentox.org/api/1.1#FeatureValue"></owl:Class><owl:Class
> rdf:about="http://www.opentox.org/api/1.1#Compound"></owl:Class><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#compound"></owl:ObjectProperty><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#dataEntry"></owl:ObjectProperty><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#values"></owl:ObjectProperty><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#feature"></owl:ObjectProperty><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#hasSource"></owl:ObjectProperty><owl:ObjectProperty
> rdf:about="http://www.opentox.org/api/1.1#acceptValue"></owl:ObjectProperty><owl:DatatypeProperty
> rdf:about="http://www.opentox.org/api/1.1#units"></owl:DatatypeProperty><owl:DatatypeProperty
> rdf:about="http://www.opentox.org/api/1.1#value"></owl:DatatypeProperty><owl:AnnotationProperty
> rdf:about="http://purl.org/dc/elements/1.1/description"></owl:AnnotationProperty><owl:AnnotationProperty
> rdf:about="http://purl.org/dc/elements/1.1/creator"></owl:AnnotationProperty><owl:AnnotationProperty
> rdf:about="http://purl.org/dc/elements/1.1/type"></owl:AnnotationProperty><owl:AnnotationProperty
> rdf:about="http://purl.org/dc/elements/1.1/title"></owl:AnnotationProperty><ot:Dataset
> rdf:about="https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/36400"><ot:dataEntry><ot:DataEntry><ot:compound><ot:Compound
> rdf:about="
> https://ambit.uni-plovdiv.bg:8443/ambit2/compound/163134/conformer/506294"></ot:Compound></ot:compound><ot:values><ot:FeatureValue><ot:feature
> rdf:resource="https://ambit.uni-plovdiv.bg:8443/ambit2/feature/178539"></ot:feature><ot:value
> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HC
> HO
> CHHHN
> CHHCC
> CHCC
> CHCN
> CCCC
> CCCN
> NCCC
> NCO
> OHN
> C(C(CCC)C(CC-H)N(CC-C))
> C(C(CCC)C(CC-H)-H(C))
> C(C(CCC)C(CN-H)-C(C-C-N))
> C(C(CCN)C(CC-H)C(CC-C))
> C(C(CCN)C(CC-H)-H(C))
> C(C(CC-H)C(CC-H)-H(C))
> C(C(CC-H)C(CC-H)-C(C-H-H-C))
> C(C(CC-H)C(CC-C)-H(C))
> C(C(CC-C)N(CC-C)-H(C))
> N(C(CCN)C(CN-H)-C(N-H-H-H))
> -H(C(CC-H))
> -H(C(CN-H))
> -H(-C(C-H-H-C))
> -H(-C(N-H-H-H))
> -H(-O(-H-N))
> -C(C(CC-C)-H(-C)-H(-C)-C(C-C-N))
> -C(C(CC-C)-C(C-H-H-C)-N(-C-O))
> -C(N(CC-C)-H(-C)-H(-C)-H(-C))
> -N(-C(C-C-N)-O(-H-N))
> -O(-H(-O)-N(-C-O))
> 
> </ot:value></ot:FeatureValue></ot:values></ot:DataEntry></ot:dataEntry></ot:Dataset><ot:Feature
> rdf:about="https://ambit.uni-plovdiv.bg:8443/ambit2/feature/178539
> "><dc:creator>Default</dc:creator><ot:hasSource>
> http://195.178.207.160/OpenTox/MNAGet</ot:hasSource><owl:sameAs
> rdf:resource="http://www.opentox.org/api/1.1#MNA
> "></owl:sameAs><ot:units></ot:units><dc:title>MNA</dc:title></ot:Feature></rdf:RDF>
> 
> 
> Nina
> 
> On 13 December 2010 10:28, Nina Jeliazkova <jeliazkova.nina at gmail.com>wrote:
> 
> > Dear Dmitry,
> >
> > On 3 December 2010 16:08, Druzhilovsky <dmitry.druzhilovsky at ibmc.msk.ru>wrote:
> >
> >> Dear Nina, All,
> >>
> >> We finished MakeMNA/MakeQNA service, and presented it:
> >>
> >> http://195.178.207.160/OpenTox/MakeMNA
> >> http://195.178.207.160/OpenTox/MakeQNA
> >>
> >> Could you check and give comments? And how could we integrate our service
> >> into ToxCreate?
> >>
> >> Example POST:
> >>
> >> curl -X POST -d
> >> dataset_uri=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/2765 -d
> >> dataset_service=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset
> >> http://195.178.207.160/OpenTox/MakeMNA
> >>
> >
> > curl -X POST -d \
> > > dataset_uri=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/2765 -d \
> > > dataset_service=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset \
> > > http://195.178.207.160/OpenTox/MakeMNA
> > <?xml version="1.0" encoding="UTF-8"?>
> > <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> >   xmlns:ns0="http://www.opentox.org/api/1.1#"
> >   xmlns:ns1="http://purl.org/dc/elements/1.1/">
> >
> >   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#DataSet">
> >     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
> >   </rdf:Description>
> >
> >   <rdf:Description rdf:about="
> > http://apps.ideaconsult.net:8080/ambit2/dataset/">
> >     <ns0:dataEntry rdf:nodeID="arc056fb1"/>
> >   </rdf:Description>
> >
> >   <rdf:Description rdf:nodeID="arc056fb1">
> >     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#DataEntry"/>
> >     <ns0:compound rdf:resource="
> > https://ambit.uni-plovdiv.bg:8443/ambit2/compound/163134/conformer/506294
> > "/>
> >     <ns0:values rdf:nodeID="MNA1"/>
> >   </rdf:Description>
> >
> >   <rdf:Description rdf:nodeID="MNA1">
> >     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#FeatureValue"/>
> >     <ns0:feature rdf:nodeID="Feature11"/>
> >     <ns0:value rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HC
> > HO
> > CHHHN
> > CHHCC
> > CHCC
> > CHCN
> > CCCC
> > CCCN
> > NCCC
> > NCO
> > OHN
> > C(C(CCC)C(CC-H)N(CC-C))
> > C(C(CCC)C(CC-H)-H(C))
> > C(C(CCC)C(CN-H)-C(C-C-N))
> > C(C(CCN)C(CC-H)C(CC-C))
> > C(C(CCN)C(CC-H)-H(C))
> > C(C(CC-H)C(CC-H)-H(C))
> > C(C(CC-H)C(CC-H)-C(C-H-H-C))
> > C(C(CC-H)C(CC-C)-H(C))
> > C(C(CC-C)N(CC-C)-H(C))
> > N(C(CCN)C(CN-H)-C(N-H-H-H))
> > -H(C(CC-H))
> > -H(C(CN-H))
> > -H(-C(C-H-H-C))
> > -H(-C(N-H-H-H))
> > -H(-O(-H-N))
> > -C(C(CC-C)-H(-C)-H(-C)-C(C-C-N))
> > -C(C(CC-C)-C(C-H-H-C)-N(-C-O))
> > -C(N(CC-C)-H(-C)-H(-C)-H(-C))
> > -N(-C(C-C-N)-O(-H-N))
> > -O(-H(-O)-N(-C-O))
> >
> > </ns0:value>
> >   </rdf:Description>
> >
> >   <rdf:Description rdf:nodeID="Feature11">
> >     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
> >     <ns0:hasSource rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
> > http://195.178.207.160/OpenTox/MNAGet</ns0:hasSource>
> >     <ns1:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string
> > ">MNA</ns1:title>
> >   </rdf:Description>
> >
> > </rdf:RDF><rdf:RDF
> >     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> >     xmlns:ot="http://www.opentox.org/api/1.1#"
> >     xmlns:bx="http://purl.org/net/nknouf/ns/bibtex#"
> >     xmlns:owl="http://www.w3.org/2002/07/owl#"
> >     xmlns:otee="http://www.opentox.org/echaEndpoints.owl#"
> >     xmlns:dc="http://purl.org/dc/elements/1.1/"
> >     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
> >     xmlns:ota="http://www.opentox.org/algorithmTypes.owl#"
> >     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#Task"/>
> >   <owl:DatatypeProperty rdf:about="
> > http://www.opentox.org/api/1.1#percentageCompleted"/>
> >   <owl:DatatypeProperty rdf:about="
> > http://www.opentox.org/api/1.1#hasStatus"/>
> >   <ot:Task rdf:about="
> > https://ambit.uni-plovdiv.bg:8443/ambit2/task/80a6cf85-a807-4347-8c94-9abc220bf039
> > ">
> >     <ot:percentageCompleted rdf:datatype="
> > http://www.w3.org/2001/XMLSchema#float"
> >     >0.0</ot:percentageCompleted>
> >     <ot:hasStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >     >Running</ot:hasStatus>
> >     <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime"
> >     >1292228310135</dc:date>
> >     <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >     >File import application/rdf+xml [1938]</dc:title>
> >   </ot:Task>
> >   <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date
> > "/>
> >   <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title
> > "/>
> > </rdf:RDF>
> >
> > curl -L -k -H "Accept:text/uri-list" "
> > https://ambit.uni-plovdiv.bg:8443/ambit2/task/80a6cf85-a807-4347-8c94-9abc220bf039
> > "
> > https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/36400
> >
> > As it could be seen, finally the URI of the dataset with MNA descriptors is
> > returned, so it works fine. However, the dataset representation, SMILES
> > string and anything, which is not ot:Task  representation and is returned
> > from the first POST call, should not be there.
> >
> > Another comment is the MNA/QNA descriptor calculation is returning Task URI
> > only after all the processing is completed and results sent to the dataset
> > service. This means , the HTTP POST call may not complete for long time, if
> > the dataset to be processed  contains more than few compounds.  OpenTox API
> > recommends to return task URI immediately after accepting the processing,
> > and then the client polls the task URI to find if it is completed.
> >
> > I have not tested how well the services work if sending multiple requests
> > in parallel, would be better if you agree to setup smokeping testing for
> > this purpose.
> >
> >
> >> But as you asked me,  if the MNA are still described as one string
> >> feature,
> >> nobody else will be able to make sense of them ... We are suggesting such
> >> structure: representation line contains only 1 or 0, which means presents
> >> or
> >> absence MNA descriptor. For each structure we'll generate fixed number of
> >> MNA descriptors for example 500. So each partners could be used this
> >> string
> >> us independent variables (which the number 500) for regression analysis.
> >> For
> >> QNA representation Chebyshev polynomials will be used. So each string will
> >> be include 100 independent variables. Variable means  Chebyshev polynomial
> >> value obtained QNA descriptor.
> >>
> >>
> > I guess the best way to handle custom formats for feature values content
> > (in addition to standard string and number types ) is to propose specific
> > MIME format and document them at OpenTox site. There might be better ways,
> > would be good to discuss during today meeting.
> >
> >
> >
> >> And more, how kind date format do you use for uploading data for lasar
> >> regression?
> >>
> >
> > I hope Christoph could answer ToxCreate and lazar related questions.
> >
> > Best regards,
> > Nina
> >
> >
> >>
> >> Best regards
> >> Dmitry
> >>
> >> _______________________________________________
> >> Development mailing list
> >> Development at opentox.org
> >> http://www.opentox.org/mailman/listinfo/development
> >>
> >
> >
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