Text-mining using OSCAR to obtain a list of Chemical names and Identifiers

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Xpath Expression

/saf/annot

Script

import java.util.ArrayList;
import java.util.HashMap;

ArrayList names = new ArrayList();
ArrayList inchis = new ArrayList();
ArrayList csids = new ArrayList();
ArrayList exNames = new ArrayList();

names.addAll(in1);
inchis.addAll(in2);
csids.addAll(in3);
exNames.addAll(in4);

String table = "
Results
Some names will unfourtunatly not produce InChIs in this service. CSID links will take you to the ChemSpider page for the substance. Name links will take you to a ChemSpider search for that name.
"; 
String tablemid = "";

for(int i = 0; i < names.size(); i++){
	String name = names.get(i);
	String inchi = inchis.get(i);
	String csid = csids.get(i);
		
	String linkStart = "";
	String linkSearch = "Search.aspx?q=";
	String nameLink = linkStart + linkSearch + name + linkEnd + name +"";
	String csLink = linkStart + csid + linkEnd + csid + "";
		
	String tablehtmlSection = "" ;
	tablemid += tablehtmlSection; // constructs a table in html
		
	}

for(int i = 0; i < exNames.size(); i++){
	String name = exNames.get(i);
	
	String linkStart = "";
	String linkSearch = "Search.aspx?q=";
	String nameLink = linkStart + linkSearch + name + linkEnd + name +"";
	
	String tablehtmlSection = "" ;
	tablemid += tablehtmlSection;
}
table += tablemid + "
Name
InChI
CSID
" + nameLink + "
" + inchi + "
" + csLink + "
" + nameLink + "
" + "
" + "
"; // completes the html string


out1 = table;

Script

import java.util.ArrayList;
import java.util.HashMap;

ArrayList oscarOutput = new ArrayList();
ArrayList oscarXML = new ArrayList();
ArrayList filteredResults = new ArrayList();
ArrayList names = new ArrayList();
ArrayList inchis = new ArrayList();
ArrayList extraResults = new ArrayList();
ArrayList extraNames = new ArrayList();


oscarOutput.addAll(in1);
int scoreStandard = Integer.parseInt(in2); 

for(String output : oscarOutput){
	if(output.contains(">CM<")){
	if(output.contains("confidence")){
		int startOfScore = output.indexOf("confidence") + 12;
		String scoreString = output.substring(startOfScore); // makes a shorter string starting at the score 
		String score = scoreString.substring(2,4); // gets confidence of chemical
		int scoreInt = Integer.parseInt(score);
		if(scoreInt >= scoreStandard){
			oscarXML.add(output);
	}
}
}
}

for(String chemXML : oscarXML){
	if(chemXML.contains("\"InChI")){
		filteredResults.add(chemXML); // adds Oscar results that have InChI component  
	} else {
			extraResults.add(chemXML);
	}
}

for(String result : filteredResults){
	int indexa = result.indexOf("surface") + 9;
	int index = result.indexOf("

Wsdl

Wsdl Operation

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

Script

  BufferedWriter out;
  if (encoding == void) {
  	out = new BufferedWriter(new FileWriter(outputFile));
  }
  else {
  	out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding)); 
  }
out.write(filecontents);
out.flush();
out.close();
outputFile = filecontents;

Value

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

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