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Thursday, December 30, 2010

The 100th Blue Obelisk 2006 paper citation

Two and a half months after the CDK milestone, the Blue Obelisk paper also reached 100 citations. Here the lucky paper is Design, Synthesis, and Preclinical Evaluation of New 5,6- (or 6,7-) Disubstituted-2-(fluorophenyl)quinolin-4-one Derivatives as Potent Antitumor Agents by Chou et al (doi:10.1021/jm100780c). The Blue Obelisk paper (doi:10.1021/ci050400b) is cited because the authors used OpenBabel. About half of the 100 citations is because OpenBabel was used, whereas OpenBabel is only mentioned as one of the Blue Obelisk-associated unprojects in the Blue Obelisk paper.

I am not sure how this habit started, but with citation practices, it is unlikely to go away. But who am I to complain....

4 comments:

  1. hello,
    Sorry for posting this here,i had started wroking with cdk ,to write a program for descriptor calculation..the code is :
    import java.util.Iterator;
    import java.util.Map;
    import org.openscience.cdk.*;
    import org.openscience.cdk.exception.CDKException;
    import org.openscience.cdk.qsar.descriptors.molecular.*;
    import org.openscience.cdk.smiles.*;
    import org.openscience.cdk.qsar.*;
    import org.openscience.cdk.qsar.result.IDescriptorResult;

    /**
    *
    * @author Hari
    * @since 19-12-2010
    * @version 1.0
    */
    public class descr {

    /**
    * @param args the command line arguments
    */
    public static void main(String[] args) throws CDKException {
    // TODO code application logic here
    BCUTDescriptor descriptor = new BCUTDescriptor();
    Molecule molecule = (Molecule) new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("NC(CO)C(=O)O");

    // The first program in wiki link for Descriptor Calculator
    DescriptorValue value = descriptor.calculate(molecule);
    IDescriptorResult theNumbers = value.getValue();
    System.out.print(theNumbers.toString()+"\n\n");

    // Second program
    DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
    engine.process(molecule);

    /**
    * The function getProperties returns a Map value. Map represents a Key Value set.
    * It is retrieved using an iterator. Since the key is of DescriptorSpecification class and the
    * value is of type DescriptorValue we have to typecast the key and value with the same while retrieving.
    * since they have not override the same to String.
    */
    Map i = molecule.getProperties();
    Iterator iterator = i.keySet().iterator();

    /**
    * The following prints the key and Value set.
    */
    while(iterator. hasNext()){
    String key = ((DescriptorSpecification)iterator.next()).getSpecificationReference().toString();
    System.out.print(key.substring(key.lastIndexOf("#")+1)+" : ");
    System.out.print(((DescriptorValue)i.get((DescriptorSpecification)iterator.next())).getValue().toString()+"\n\n");
    }

    }

    }


    the output is different for windows and linux. while i get only a bcut descriptor o/p for standalone and netbeans 6.8 in linux, around 40 descriptors are given as o/p in windows using netbeans 6.8... please advice

    ReplyDelete
  2. Hi Hari, I noted your blog, but I cannot comment there...

    ReplyDelete
  3. hai egon,
    could u suggest where i could blog my query?

    ReplyDelete
  4. Your blog post at http://cdkhari.blogspot.com/2011/01/cdk-varying-out-puts.html is fine. I seem now able to leave a comment.

    ReplyDelete