BioCyc:Reaction Scheme
Created: 2013-09-06 13:26:45
Download WorkflowThe purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps:
- determine all the reactions that the given metabolite participates in
- determine all the compounds that participate in these reactions
- filter certain compounds like H2O, ATP etc to avoid non-specific connections
- determine all the reactions that the compounds passing through step 3 participate in
- determine the enzymes that drive the reactions from step 4
- determine genes corresponding to the enzymes in step 5
- store the entrez gene ids as a text file
Preview
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3744/download?version=1
[ More Info
]
Taverna is available from http://taverna.sourceforge.net/
If you are having problems downloading it in Taverna, you may need to provide your username and password in the URL so that Taverna can access the Workflow:
Replace http:// in the link above with http://yourusername:yourpassword@
Workflow Components
Authors (1)
| Harish Dharuri |
Titles (1)
| BioCyc:Reaction Scheme |
Descriptions (1)
| The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps: 1. determine all the reactions that the given metabolite participates in 2. determine all the compounds that participate in these reactions 3. filter certain compounds like H2O, ATP etc to avoid non-specific connections 4. determine all the reactions that the compounds passing through step 3 participate in 5. determine the enzymes that drive the reactions from step 4 6. determine genes corresponding to the enzymes in step 5 7. store the entrez gene ids as a text file |
Dependencies (0)
None
Inputs (2)
| Name | Description |
|---|---|
| input_compound | The input for the workflow is a Biocyc compound name, for example: L-arginine or L-alanine etc |
| path_to_output_file | This takes the input of the local directory where the user wants to store the output result of the workflow. |
Processors (28)
| Name | Type | Description |
|---|---|---|
| REST_Service_Reactions_I | rest | REST service: The function of this component is to access the BioCyc database with the user input compound and return the details of the compound in the form of an xml document |
| XPath_Service | xpath |
Parse the xml document and extract reactions. Xpath Expression/ptools-xml/Compound/*/Reaction/@frameid |
| XML_Error_Check | beanshell |
Checks for known xml errors Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
for(int i=0; i < in1.size(); i++) {
tmp.add(in1.get(i).toString().replace("#<","#"));
}
result = tmp;
|
| Flatten_List | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Query_for_compounds_of_reaction | beanshell |
Build the query to return compounds that participate in a given reaction. Scriptout1="[x:y:=human~" + "\"" + in1 + "\"" + ",x<-(compounds-of-reaction y)]" |
| REST_Service_Compounds_I | rest | REST Service: Functions to access the BioCyc database and extract the compounds for the given reactions and return an xml document. |
| XML_Error_Check_2 | beanshell |
Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
for(int i=0; i < in1.size(); i++) {
tmp.add(in1.get(i).toString().replace("#<","#"));
}
result = tmp;
|
| XPath_Service_2 | xpath |
Xpath Expression/ptools-xml/Compound/common-name |
| Flatten_List_2 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Remove_String_Duplicates | 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);
}
}
|
| Filter_compounds | beanshell |
Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
for(int i=0; i < in1.size(); i++) {
if(!in1.get(i).toString().equals("5'-deoxyadenosine") && !in1.get(i).toString().equals("a 2,3,4-saturated fatty acyl CoA") && !in1.get(i).toString().equals("a carboxylate") && !in1.get(i).toString().equals("a reduced electron acceptor") && !in1.get(i).toString().equals("a standard α amino acid") && !in1.get(i).toString().equals("a sugar") && !in1.get(i).toString().equals("acetyl-CoA") && !in1.get(i).toString().equals("an acyl-CoA") && !in1.get(i).toString().equals("an oligopeptide") && !in1.get(i).toString().equals("ammonia") && !in1.get(i).toString().equals("ADP") && !in1.get(i).toString().equals("ADP-ribose") && !in1.get(i).toString().equals("AMP") && !in1.get(i).toString().equals("ATP") && !in1.get(i).toString().equals("an aldehyde") && !in1.get(i).toString().equals("an oxidized electron acceptor") && !in1.get(i).toString().equals("bicarbonate")
&& !in1.get(i).toString().equals("CMP") && !in1.get(i).toString().equals("CO2") && !in1.get(i).toString().equals("coenzyme A") && !in1.get(i).toString().equals("CTP") && !in1.get(i).toString().equals("diphosphate") && !in1.get(i).toString().equals("GDP") && !in1.get(i).toString().equals("GMP") && !in1.get(i).toString().equals("H2O") && !in1.get(i).toString().equals("H+") && !in1.get(i).toString().equals("hydrogen peroxide")
&& !in1.get(i).toString().equals("Na+") && !in1.get(i).toString().equals("NAD+") && !in1.get(i).toString().equals("NADP+") && !in1.get(i).toString().equals("NAD(P)+") && !in1.get(i).toString().equals("NADH") && !in1.get(i).toString().equals("NADPH") && !in1.get(i).toString().equals("NAD(P)H") && !in1.get(i).toString().equals("nicotinate adenine dinucleotide") && !in1.get(i).toString().equals("nicotinate adenine mononucleotide") && !in1.get(i).toString().equals("nitric oxide") && !in1.get(i).toString().equals("oxygen") && !in1.get(i).toString().equals("phosphate") && !in1.get(i).toString().equals("S2-") && !in1.get(i).toString().equals("sulfate") && !in1.get(i).toString().equals("UDP") && !in1.get(i).toString().equals("UTP"))
{
tmp.add(in1.get(i).toString());
}
}
result = tmp; |
| Query_for_reactions_of_compound | beanshell |
Scriptout1="[x:x<-human^^compounds,x^name=" + "\"" +in1+ "\""+"]" |
| REST_Service_Reactions_II | rest | REST Service: Functions to access the BioCyc database and extract the reactions for the given compounds and return an xml document. |
| XML_Error_Check_3 | beanshell |
Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
for(int i=0; i < in1.size(); i++) {
tmp.add(in1.get(i).toString().replace("#<","#"));
}
result = tmp;
|
| XPath_Service_3 | xpath |
Xpath Expression/ptools-xml/Compound/*/Reaction/@frameid |
| Flatten_List_3 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| REST_Service_Genes | rest | REST Service: Functions to access the BioCyc database and extract the genes/enzymes that catalyze the set of input reactions and return an xml document. |
| XML_Error_Check_5 | beanshell |
Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
for(int i=0; i < in1.size(); i++) {
tmp.add(in1.get(i).toString().replace("#<","#"));
}
result = tmp;
|
| XPath_Service_5 | xpath |
Xpath Expression/ptools-xml/Gene/common-name |
| hgnc | biomart | Biomart service to convert HGNC symbols to entrez ids. |
| Create_and_populate_temporary_file_2 | beanshell |
ScriptFile f = File.createTempFile("taverna", ".tmp");
BufferedWriter writer = new BufferedWriter(new FileWriter(f));
writer.write(content);
writer.close();
filepath = f.getCanonicalPath(); |
| Concatenate_Files_2 | localworker |
ScriptBufferedReader getReader (String fileUrl) throws IOException {
InputStreamReader reader;
try {
reader = new FileReader(fileUrl);
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
reader = new InputStreamReader (url.openStream());
}
return new BufferedReader(reader);
}
String NEWLINE = System.getProperty("line.separator");
boolean displayResults = false;
if (displayresults != void) {
displayResults = Boolean.valueOf(displayresults).booleanValue();
}
StringBuffer sb = new StringBuffer(2000);
if (outputfile == void) {
throw new RuntimeException("The 'outputfile' parameter cannot be null");
}
if (filelist == null) {
throw new RuntimeException("The 'filelist' parameter cannot be null");
}
String str = null;
Writer writer = new FileWriter(outputfile);
for (int i = 0; i < filelist.size(); i++) {
BufferedReader reader = getReader(filelist.get(i));
while ((str = reader.readLine()) != null) {
writer.write(str);
writer.write(NEWLINE);
if (displayResults) {
sb.append(str);
sb.append(NEWLINE);
}
}
reader.close();
}
writer.flush();
writer.close();
if (displayResults) {
results= sb.toString();
}
|
| Query_for_reaction_to_genes | beanshell |
Scriptout1="[x:y:=human~"+"\""+ in1 + "\"" + ",x<-(reaction-to-genes y)]" |
| Remove_String_Duplicates_3 | 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);
}
}
|
| Flatten_List_6 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Remove_String_Duplicates_4 | 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);
}
}
|
| Flatten_List_7 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| query_for_REST_service | beanshell |
This builds the query with the input compound for the REST interface. Scriptout1="[x:x<-human^^compounds,x^name=" + "\"" + in1 + "\"]" |
Beanshells (10)
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| XML_Error_Check | Checks for known xml errors | in1 | result |
| Query_for_compounds_of_reaction | Build the query to return compounds that participate in a given reaction. | in1 | out1 |
| XML_Error_Check_2 | in1 | result | |
| Filter_compounds | in1 | result | |
| Query_for_reactions_of_compound | in1 | out1 | |
| XML_Error_Check_3 | in1 | result | |
| XML_Error_Check_5 | in1 | result | |
| Create_and_populate_temporary_file_2 | content | filepath | |
| Query_for_reaction_to_genes | in1 | out1 | |
| query_for_REST_service | This builds the query with the input compound for the REST interface. | in1 | out1 |
Outputs (0)
None
Datalinks (29)
| Source | Sink |
|---|---|
| query_for_REST_service:out1 | REST_Service_Reactions_I:query |
| XML_Error_Check:result | XPath_Service:xml_text |
| REST_Service_Reactions_I:responseBody | XML_Error_Check:in1 |
| XPath_Service:nodelist | Flatten_List:inputlist |
| Flatten_List:outputlist | Query_for_compounds_of_reaction:in1 |
| Query_for_compounds_of_reaction:out1 | REST_Service_Compounds_I:query |
| REST_Service_Compounds_I:responseBody | XML_Error_Check_2:in1 |
| XML_Error_Check_2:result | XPath_Service_2:xml_text |
| XPath_Service_2:nodelist | Flatten_List_2:inputlist |
| Flatten_List_2:outputlist | Remove_String_Duplicates:stringlist |
| Remove_String_Duplicates:strippedlist | Filter_compounds:in1 |
| Filter_compounds:result | Query_for_reactions_of_compound:in1 |
| Query_for_reactions_of_compound:out1 | REST_Service_Reactions_II:query |
| REST_Service_Reactions_II:responseBody | XML_Error_Check_3:in1 |
| XML_Error_Check_3:result | XPath_Service_3:xml_text |
| XPath_Service_3:nodelist | Flatten_List_3:inputlist |
| Query_for_reaction_to_genes:out1 | REST_Service_Genes:query |
| REST_Service_Genes:responseBody | XML_Error_Check_5:in1 |
| XML_Error_Check_5:result | XPath_Service_5:xml_text |
| Remove_String_Duplicates_4:strippedlist | hgnc:hgnc.gd_app_sym_filter |
| Flatten_List_7:outputlist | Create_and_populate_temporary_file_2:content |
| Create_and_populate_temporary_file_2:filepath | Concatenate_Files_2:filelist |
| path_to_output_file | Concatenate_Files_2:outputfile |
| Remove_String_Duplicates_3:strippedlist | Query_for_reaction_to_genes:in1 |
| Flatten_List_3:outputlist | Remove_String_Duplicates_3:stringlist |
| XPath_Service_5:nodelist | Flatten_List_6:inputlist |
| Flatten_List_6:outputlist | Remove_String_Duplicates_4:stringlist |
| hgnc:hgnc.gd_pub_eg_id | Flatten_List_7:inputlist |
| input_compound | query_for_REST_service:in1 |
Coordinations (0)
None
Workflow Type
Version 1
(of 1)
Shared with Groups (0)
None
Log in to add to one of your Packs
Statistics
Version History
Reviews
(0)
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
No comments yet
Log in to make a comment