Mining the Kegg pathway database with the top hits from a GWAS, thereby predicting which gene regulatory pathways may be altered as a result of genetic mutations in a subpopulation.
Created: 2012-08-29 18:28:47
Last updated: 2013-05-15 14:37:36
Download WorkflowGenome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow is to take the GWAS output consisting of SNP-metabolite associations and return genes present in the vicinity of the SNP ( for example, ± 100 kb of the snp) and the pathways that these genes participate in. The user is provided with the choice of setting the flanking width to interrogate around the SNP.
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Workflow Components
Authors (1)
| Harish Dharuri |
Titles (1)
| Mining the Kegg pathway database with the top hits from a GWAS. |
Descriptions (1)
| Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow is to take the GWAS output consisting of SNP-metabolite associations and return genes present in the vicinity of the SNP ( for example, ± 100 kb of the snp) and the pathways that these genes participate in. The user is provided with the choice of setting the flanking width to interrogate around the SNP. |
Dependencies (0)
None
Inputs (3)
| Name | Description |
|---|---|
| path_to_input_file | This takes the input of the local directory where the user has stored the GWAS output. It is necessary that the SNP IDs be present in the first column of the input file. |
| path_to_output_file | This takes the input of the local directory where the user wants to store the output result of the workflow. |
| set_width | The allows the user to set the flanking width for the gene for determining SNPs |
Processors (24)
| Name | Type | Description |
|---|---|---|
| extract_snp_id | beanshell |
This extracts the contents (snp_ids) of the first column from the input.It is important that the first column contains SNP IDs for this reason. Scriptimport java.util.*;
String [] line = string.split("\t");
out1=line[0].trim(); |
| Split_string_into_string_list_by_regular_expression | localworker |
This service splits the string value into a string list at every occurrence of the specified regular expression. The regular expression provided in this case is a new line: "\n" 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]);
}
}
|
| regex_value | stringconstant |
Value\n |
| hsapiens_snp | biomart | This is a Biomart service that takes the SNP ID as the input and returns chromosome name, and the position of the SNP. |
| Flatten_List | localworker |
This service flattens the inputlist by one level. It returns the result of the flattening. 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); |
| Flatten_List_2 | localworker |
This service flattens the inputlist by one level. It returns the result of the flattening. 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); |
| input_chr_position | beanshell |
The purpose of this beanshell is to manipulate the start and end positions based on the flanking width provided by the user. Scriptimport java.util.*;
List tmp_end = new ArrayList();
List tmp_start = new ArrayList();
width =Integer.parseInt(in1.get(0));
int out_end=0;
int out_start=0;
for(int i=0; i < in2.size(); i++) {
value_pos = Integer.parseInt(in2.get(i));
out_end = value_pos + width;
out_start = value_pos - width;
tmp_end.add(out_end);
tmp_start.add(out_start);
}
end_out = tmp_end;
start_out = tmp_start;
chr_out = chr_in;
|
| hsapiens_gene_ensembl | biomart | This is a Biomart service that takes the chromosome name and start and end positions and returns genes (entrez gene id) present in the region. |
| align_snp_gene_and_extract_gene_id | beanshell |
This beanshell aligns the input snp ids with the corresponding genes present in the vicinity. Scriptimport java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
String in1Trim = in1.trim();
String out=in1Trim+"\t"+in2;
String [] out_array = out.split("\t");
String gene_out =out_array[out_array.length-1];
int aa = gene_out.indexOf("[");
int bb = gene_out.indexOf("]");
String S1 = gene_out.substring(aa+1,bb);
int cc = bb-aa;
j=0;
i =S1.indexOf(",");
if (i<0 && cc==1){
tmp.add(in1Trim+"\t"+"-1");
}
else if (i<0 && cc>1) {
tmp.add(in1Trim+"\t"+S1);
}
else {
String [] line = S1.split(",");
while(j < line.length) {
tmp.add(in1Trim+"\t"+line[j]);
j++;
}
}
out1=tmp; |
| Convert_to_Kegg_id | beanshell |
The input to btit (which provides gene information from the kegg database) is a Kegg gene id. To convert entrez gene ids to Kegg ids "hsa:" is concatenated to the entrez gene id. Scriptimport java.util.*;
String [] line = string.split("\t");
String gene = line[line.length-1];
String gene1=gene.trim();
if (gene1==-1){
out1="";
}
else {
out1="hsa:"+gene1;
}
|
| btit | wsdl |
The input for this service is Kegg gene id in the form of (for example) hsa:1234. It returns the gene name and definitions of the given entry id. Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationbtit |
| extract_gene_name | beanshell |
The purpose of this workflow is to extract gene names from the "btit" output. Scriptimport java.util.*;
String [] line = string.split(",");
String ID_Gene = line[0];
int aa = ID_Gene.indexOf(" ");
String gene_noTrim = ID_Gene.substring(aa+1);
String gene = gene_noTrim.trim();
int bb = gene.indexOf(";");
if (bb<0){
out1=gene.trim();
}
else {
String gene1 = gene.substring(0,bb);
out1=gene1.trim();
}
|
| align_snp_gene_name | beanshell |
This beanshell aligns the input snp ids with the corresponding genes (in the form of HGNC names) present in the vicinity. Scriptimport java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
String in1Trim = in1.trim();
String out=in1Trim+"\t"+in2;
String [] out_array = out.split("\t");
String gene_out =out_array[out_array.length-1];
int aa = gene_out.indexOf("[");
int bb = gene_out.indexOf("]");
String S1 = gene_out.substring(aa+1,bb);
int cc = bb-aa;
j=0;
i =S1.indexOf(",");
if (i<0 && cc==1){
tmp.add(in1Trim+"\t"+"-1");
}
else if (i<0 && cc>1) {
tmp.add(in1Trim+"\t"+S1);
}
else {
String [] line = S1.split(",");
while(j < line.length) {
tmp.add(in1Trim+"\t"+line[j]);
j++;
}
}
out1=tmp; |
| get_pathways_by_genes | wsdl |
Search all pathways which include all the given genes. Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_pathways_by_genes |
| regex_value_1 | stringconstant |
Value\n |
| Split_string_into_string_list_by_regular_expression_2 | localworker |
This service splits the string value into a string list at every occurrence of the specified regular expression. The regular expression provided in this case is a new line: "\n" 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]);
}
}
|
| Flatten_List_3 | localworker |
This service flattens the inputlist by one level. It returns the result of the flattening. 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); |
| Flatten_List_6 | localworker |
This service flattens the inputlist by one level. It returns the result of the flattening. 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); |
| btit_2_2 | wsdl |
Retrieve definitions of given pathways on the Kegg pathway database. Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationbtit |
| align_snp_gene_name_pwy_ids_2 | beanshell |
This beanshell aligns the input snp ids with the corresponding genes (in the form of HGNC names) present in the vicinity and the pathways that these genes participates in. Scriptimport java.util.List;
import java.util.ArrayList;
List tmp = new ArrayList();
String in1Trim = in1.trim();
String out=in1Trim+"\t"+in2;
String [] out_array = out.split("\t");
String gene_out =out_array[out_array.length-1];
int aa = gene_out.indexOf("[");
int bb = gene_out.indexOf("]");
String S1 = gene_out.substring(aa+1,bb);
int cc = bb-aa;
j=0;
i =S1.indexOf(",");
if (i<0 && cc==1){
tmp.add(in1Trim+"\t"+"-1");
}
else if (i<0 && cc>1) {
tmp.add(in1Trim+"\t"+S1);
}
else {
String [] line = S1.split(",");
while(j < line.length) {
tmp.add(in1Trim+"\t"+line[j]);
j++;
}
}
out1=tmp; |
| Flatten_List_5_2 | localworker |
This service flattens the inputlist by one level. It returns the result of the flattening. 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); |
| Create_and_populate_temporary_file_2 | beanshell |
This service creates a temporary file in a local tmp directory. 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 |
This service examines the files whose paths or URLs are specified in the filelist. The content of those files is concatenated. 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();
}
|
| Read_Text_File | localworker |
This service reads the text file at the specified file path or URL and returns the file's content. ScriptBufferedReader getReader (String fileUrl, String encoding) throws IOException {
InputStreamReader reader;
try {
if (encoding == null) {
reader = new FileReader(fileUrl);
} else {
reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
}
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
if (encoding == null) {
reader = new InputStreamReader (url.openStream());
} else {
reader = new InputStreamReader (url.openStream(), encoding);
}
}
return new BufferedReader(reader);
}
StringBuffer sb = new StringBuffer(4000);
if (encoding == void) {
encoding = null;
}
BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");
while ((str = in.readLine()) != null) {
sb.append(str);
sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
|
Beanshells (8)
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| extract_snp_id | This extracts the contents (snp_ids) of the first column from the input.It is important that the first column contains SNP IDs for this reason. | string | out1 |
| input_chr_position | The purpose of this beanshell is to manipulate the start and end positions based on the flanking width provided by the user. |
chr_in in2 in1 |
chr_out end_out start_out |
| align_snp_gene_and_extract_gene_id | This beanshell aligns the input snp ids with the corresponding genes present in the vicinity. |
in1 in2 |
out1 |
| Convert_to_Kegg_id | The input to btit (which provides gene information from the kegg database) is a Kegg gene id. To convert entrez gene ids to Kegg ids "hsa:" is concatenated to the entrez gene id. | string | out1 |
| extract_gene_name | The purpose of this workflow is to extract gene names from the "btit" output. | string | out1 |
| align_snp_gene_name | This beanshell aligns the input snp ids with the corresponding genes (in the form of HGNC names) present in the vicinity. |
in1 in2 |
out1 |
| align_snp_gene_name_pwy_ids_2 | This beanshell aligns the input snp ids with the corresponding genes (in the form of HGNC names) present in the vicinity and the pathways that these genes participates in. |
in1 in2 |
out1 |
| Create_and_populate_temporary_file_2 | This service creates a temporary file in a local tmp directory. | content | filepath |
Outputs (0)
None
Datalinks (32)
| Source | Sink |
|---|---|
| Split_string_into_string_list_by_regular_expression:split | extract_snp_id:string |
| regex_value:value | Split_string_into_string_list_by_regular_expression:regex |
| Read_Text_File:filecontents | Split_string_into_string_list_by_regular_expression:string |
| extract_snp_id:out1 | hsapiens_snp:hsapiens_snp.snp_filter_filter |
| hsapiens_snp:hsapiens_snp.chr_name | Flatten_List:inputlist |
| hsapiens_snp:hsapiens_snp.chrom_start | Flatten_List_2:inputlist |
| Flatten_List:outputlist | input_chr_position:chr_in |
| Flatten_List_2:outputlist | input_chr_position:in2 |
| set_width | input_chr_position:in1 |
| input_chr_position:chr_out | hsapiens_gene_ensembl:hsapiens_gene_ensembl.chromosome_name_filter |
| input_chr_position:end_out | hsapiens_gene_ensembl:hsapiens_gene_ensembl.end_filter |
| input_chr_position:start_out | hsapiens_gene_ensembl:hsapiens_gene_ensembl.start_filter |
| Split_string_into_string_list_by_regular_expression:split | align_snp_gene_and_extract_gene_id:in1 |
| hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene | align_snp_gene_and_extract_gene_id:in2 |
| align_snp_gene_and_extract_gene_id:out1 | Convert_to_Kegg_id:string |
| Convert_to_Kegg_id:out1 | btit:string |
| btit:return | extract_gene_name:string |
| Split_string_into_string_list_by_regular_expression:split | align_snp_gene_name:in1 |
| extract_gene_name:out1 | align_snp_gene_name:in2 |
| Split_string_into_string_list_by_regular_expression_2:split | get_pathways_by_genes:genes_id_list |
| regex_value_1:value | Split_string_into_string_list_by_regular_expression_2:regex |
| Flatten_List_6:outputlist | Split_string_into_string_list_by_regular_expression_2:string |
| align_snp_gene_name:out1 | Flatten_List_3:inputlist |
| Convert_to_Kegg_id:out1 | Flatten_List_6:inputlist |
| get_pathways_by_genes:return | btit_2_2:string |
| Flatten_List_3:outputlist | align_snp_gene_name_pwy_ids_2:in1 |
| btit_2_2:return | align_snp_gene_name_pwy_ids_2:in2 |
| align_snp_gene_name_pwy_ids_2:out1 | Flatten_List_5_2:inputlist |
| Flatten_List_5_2: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 |
| path_to_input_file | Read_Text_File:fileurl |
Coordinations (0)
None
Workflow Type
Version 1 (earliest)
(of 2)
Shared with Groups (1)
Statistics
Version History
In chronological order:
-
Created by Harish Dharuri on Wednesday 29 August 2012 18:28:46 (UTC)
-
Created by Harish Dharuri on Wednesday 15 May 2013 14:37:36 (UTC)
Revision comment:This version uses the KEGG REST services [http://www.kegg.jp/kegg/rest/keggapi.html].
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Beautifully annotated and runs without problems with its example inputs on Taverna 2.4 (14 september 2012).