Search Europe PMC and get ChEBI annotations
Created: 2018-02-09 14:09:48
Last updated: 2018-02-12 16:12:40
This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.
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Workflow Components
Authors (1)
Titles (1)
| Search Europe PMC and get ChEBI annotations |
Descriptions (1)
| This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API. |
Dependencies (0)
Inputs (1)
| Name |
Description |
| Query |
Europe PMC query string
|
Processors (13)
| Name |
Type |
Description |
| searchPublications_and_get_ChEBIs |
workflow |
|
| getAnnotations |
rest |
|
| Flatten_Sources_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); |
| Flatten_Ids_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); |
| Remove_Sources_header |
localworker |
Scriptfilteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (item.matches(regex)) {
filteredlist.add(item);
}
}
|
| MED_or_PMC |
stringconstant |
ValueMED|PMC |
| Remove_Ids_header |
localworker |
Scriptfilteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (item.matches(regex)) {
filteredlist.add(item);
}
}
|
| number |
stringconstant |
Value[0-9]+ |
| extract_URI |
jsonpath |
|
| Flatten_URI_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); |
| Write_Text_File |
localworker |
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;
|
| filename |
stringconstant |
ValueC:\tmp\from_taverna.txt |
| Merge_String_List_to_a_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();
|
Beanshells (3)
| Name |
Description |
Inputs |
Outputs |
| Build_Query |
This build_query BeanShell constructs the Europe PMC search query for a single protein in UniProt. |
nextCursorMark
Query
Iteration
|
queryString
cursorMark
Iteration
|
| add_sources |
|
new_Sources
Sources
|
Sources
|
| add_ids |
|
Ids
new_Ids
|
Ids
|
Outputs (4)
| Name |
Description |
| Sources |
|
| hitCount |
|
| annotations |
|
| Ids |
|
Datalinks (18)
| Source |
Sink |
| Query |
searchPublications_and_get_ChEBIs:Query |
| Remove_Sources_header:filteredlist |
getAnnotations:source |
| Remove_Ids_header:filteredlist |
getAnnotations:id |
| searchPublications_and_get_ChEBIs:Sources |
Flatten_Sources_List:inputlist |
| searchPublications_and_get_ChEBIs:Ids |
Flatten_Ids_List:inputlist |
| Flatten_Sources_List:outputlist |
Remove_Sources_header:stringlist |
| MED_or_PMC:value |
Remove_Sources_header:regex |
| Flatten_Ids_List:outputlist |
Remove_Ids_header:stringlist |
| number:value |
Remove_Ids_header:regex |
| getAnnotations:responseBody |
extract_URI:json_text |
| extract_URI:nodelist |
Flatten_URI_List:inputlist |
| filename:value |
Write_Text_File:outputFile |
| Merge_String_List_to_a_String:concatenated |
Write_Text_File:filecontents |
| Flatten_URI_List:outputlist |
Merge_String_List_to_a_String:stringlist |
| searchPublications_and_get_ChEBIs:Sources |
Sources |
| searchPublications_and_get_ChEBIs:hitCount |
hitCount |
| Write_Text_File:outputFile |
annotations |
| searchPublications_and_get_ChEBIs:Ids |
Ids |
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License
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licensed under:
Version 1 (earliest)
(of 3)
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