| Name |
Type |
Description |
| regex |
stringconstant |
Value\n |
| remove_nulls |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
} |
| gene_and_abstract |
beanshell |
ScriptString[] split = abstracts.split("\n");
String pathway_name = pathway;
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
nonEmpty.add(trimmed);
}
String output = ">> " + pathway_name + "\n";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
} |
| split_search_terms |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
| merge_outputs_2 |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| Search_PubMed |
workflow |
|
| clean_text |
workflow |
|
| regular_expression |
stringconstant |
Value\n |
| Remove_duplicate_genes |
localworker |
ScriptList strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (strippedlist.contains(item) == false) {
strippedlist.add(item);
}
}
|
| split_gene_names |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
| remove_Nulls_2 |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
} |
| Merge_string_list_to_string |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| xpath |
stringconstant |
Value/*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id'] |
| run_eSearch |
wsdl |
Wsdlhttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdlWsdl Operationrun_eSearch |
| min_date |
stringconstant |
Value2000/01/01 |
| extractPMID |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| remove_Nulls_4 |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
} |
| concat_abstract_ids |
beanshell |
ScriptString id = id.trim();
String abstract_text = abstract_text.trim();
String[] abstract_array = abstract_text.split("\n");
String abstract_amended = "";
if(abstract_array.length > 1)
{
abstract_amended = abstract_array[0] + " ";
for(int i = 1; i < abstract_array.length; i++)
{
abstract_amended = abstract_amended + abstract_array[i] + " ";
}
}
else
{
abstract_amended = abstract_array[0];
}
String date_text = date_text.trim();
String output = "";
output = id + "\t" + date_text + "\t" + abstract_amended; |
| max_return_phenotype |
stringconstant |
Value5000 |
| pubmed_database |
stringconstant |
Valuepubmed |
| merge_phenotype_abstracts |
beanshell |
ScriptString[] split = abstracts.split("\n");
String phenotype_term = phenotype.trim();
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
// String mytext = split[i].substring(split[i].indexOf(0), split[i].indexOf(" AND "));
nonEmpty.add(trimmed);
}
String output = ">> " + phenotype_term + "\n";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
} |
| merge_abstracts |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| max_date |
stringconstant |
Value2011/01/31 |
| parametersXML_eSearch |
xmlsplitter |
|
| merge_abstract_ids |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| merge_dates |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| Fetch_Abstracts |
workflow |
|
| clean_text_3 |
workflow |
|
| Encode_byte_to_base64 |
localworker |
Scriptimport org.apache.commons.codec.binary.Base64;
base64 = new String(Base64.encodeBase64(bytes)); |
| merge_strings_2 |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| regex_3 |
stringconstant |
Value\n |
| xpath_2 |
stringconstant |
Value/*[local-name(.)='generateTerminologyResponse']/*[local-name(.)='return'] |
| extract_abstracts |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 1; i < split.length; i++)
{
String trimmed = split[i].trim();
String[] split_2 = trimmed.split("\t");
if(split_2.length == 3)
{
nonEmpty.add(split_2[2]);
}
}
String output_search = split[0] + "\n";
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
} |
| merge_search_and_terms |
beanshell |
ScriptString term_input = terms.trim();
String search_input = search_term.trim();
String output = "";
output = search_input + "\n" + term_input; |
| extract_Terms_2 |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| merge_strings |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| remove_Nulls_5 |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
} |
| Remove_duplicate_strings_2 |
localworker |
ScriptList strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (strippedlist.contains(item) == false) {
strippedlist.add(item);
}
}
|
| split_by_regex |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
| clean_text_4 |
soaplab |
Endpointhttp://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text |
| pubmed_database_2 |
stringconstant |
Valuepubmed |
| xpath_3 |
stringconstant |
Value/*[local-name(.)='eSearchResult']/*[local-name(.)='Count'] |
| count |
stringconstant |
Valuecount |
| xpath_count |
stringconstant |
Value/*[local-name(.)='eInfoResult']/*[local-name(.)='DbInfo']/*[local-name(.)='Count'] |
| eSearch_database |
stringconstant |
Valuepubmed |
| regular_expression_2 |
stringconstant |
Value\n |
| extract_terms_3 |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 1; i < split.length; i++)
{
String trimmed = split[i].trim();
// if((trimmed.contains("=")) || (trimmed.contains("-")))
// {
// next;
// }
// else
// {
// String[] trimmed_array = trimmed.split("\t");
// String term = trimmed_array[0];
nonEmpty.add(trimmed);
// }
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
} |
| merge_term_count |
beanshell |
ScriptString term_input = term.trim();
String count_input = count.trim();
String output = "";
output = term_input + "\t" + count_input; |
| split_extracted_terms |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
| merge_pubmed_count |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| merge_extracted |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| merge_list |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
| extractCount_2 |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| extractCount |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
| parametersXML_1 |
xmlsplitter |
|
| run_eInfo |
wsdl |
Wsdlhttp://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdlWsdl Operationrun_eInfo |
| run_eSearch_2 |
wsdl |
Wsdlhttp://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdlWsdl Operationrun_eSearch |
| run_eSearch_request |
xmlsplitter |
|
| GENE_RankPhenotypeTerms |
workflow |
|
| max_return_gene |
stringconstant |
Value500 |
| generateTerminology |
wsdl |
Wsdlhttp://projects.biotec.tu-dresden.de/DOG4DAG_TAVERNA/services/GoPubMedTermGeneration?wsdlWsdl OperationgenerateTerminology |
| generateTerminology_input |
xmlsplitter |
|
| applicationCode_value |
stringconstant |
Value20110209_taverna |
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