Diff for "CyThesaurus_Plugin"

[UNDER CONSTRUCTION]

Introduction

CyThesaurus is a Cytoscape plugin providing identifier mapping services based on various resources. Currently the plugin support ID mapping resources from delimited text, PGDB file and BioMart web service. This plugin utilized BridgeDb API.

Use Cases

5 related use cases have been identified on Bader Lab ID Mapping page. 2 of them are closely related to this project:

• Unification during dataset merging: During a merge operation e.g. of two protein-protein interaction datasets from independently created databases, it is vital to recognize that two protein objects, one from each data source, represent the same protein molecule, even if the protein objects don’t share any database accession numbers. Unification requires knowledge of record type e.g. you cannot reliably use a gene ID to unify proteins (mostly because splice variants exist).

• Identifier translation: Some analysis methods require specific translations from one set of identifiers to another. For instance, our 'activity centers' analysis requires translation from protein or gene identifiers in a pathway database to Affymetrix probe set identifiers or other gene expression array platform identifiers.

Supported ID Mapping Resources

File- based

Delimited text file

• File format (e.g. http://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt):

  • Each column for one ID type
  • Each row except the first one represents IDs of different types mapping to each other
  • First row contains ID types
  • Multiple IDs are allowed to be contained in one cell (One to many mapping, or IDs of the same type maps to each other). Use special character (e.g., ';', '/', etc, or user defined) to separate IDs.

RDB based

PGDB file

• Gene database schema: http://www.bridgedb.org/wiki/GeneDatabaseLayout

• Gene databases are available at http://bridgedb.org/data/gene_database/

Web service based

BioMart web service

BioMart web service has been utilized to provide ID mapping service in this plugin.

BridgeDb web service

Being developed.

PICR web service

Being developed.

Code Base

Currently the plugin is based on Cytoscape 2.6. Porting to Cytoscape 3.0 is in plan.

ID mapping service for other plugin

An inter-plugin communication module was developed to support CyThesaurus plugin providing ID mapping services to other plugins. It is recommended that other plugins, who need to request ID mapping services from CyThesaurus, include the package cytoscape-plugins-comm ( cytoscape-plugins-comm.jar, javadoc, src). The following services are supported.

Supported ID mapping services

1. Test request: Test if the services are available.

   •    1   #!java
        2     String sender = pluginName;
        3     String receiver = "CyThesaurus"; // plugin name when passing messages
        4     String msgType = Message.MSG_TYPE_TEST; // indicate what this message requests for
        5     String msgId = receiver + System.currentTimeMillis();
        6     Message msg = new Message(msgId , sender, receiver, msgType , null);
        7     List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
        8     if (!response.isEmpty()) {
        9         // the ID mapping services are available
       10     }
       11 
     

2. ID mapping services list: get all the ID mapping services

   •    1   #!java
        2     String receiver = "CyThesaurus"; // plugin name when passing messages
        3     Set<String> types = PluginsCommunicationSupport.getMessageTypes(receiver);
        4     if (!types.isEmpty()) {
        5         // the ID mapping services are available
        6     } else {
        7         // ID mapping services are unavailable
        8     }
        9 
     

3. ID mapping request: Request to mapping the IDs of source ID types in one attribute to the target ID types and save in the target attribute

   •    1   #!java
        2     String sender = pluginName;
        3     String receiver = "CyThesaurus";
        4     String msgType = "REQUEST_MAPPING"; // request for ID mapping service
        5     String msgId = receiver + System.currentTimeMillis();
        6     Map content = new HashMap();
        7     content.put("NETWORK_ID", new String[]{"net1", "net2"}); // if NETWORK_ID is not specified, 
        8                                         //ID mapping will be performed on all networks in session
        9     // or content.put("NETWORK_ID", "net1");
       10     content.put("SOURCE_ATTR", new String[]{"Attr1", "Attr2"});
       11     // or content.put("SOURCE_ATTR", "ID");
       12     content.put("SOURCE_ID_TYPE", new String[]{"Type1","Type2"}); // if SOURCE_ID_TYPE is not specified, 
       13                                                           //all supported source id types will be used
       14     // or content.put("SOURCE_ID_TYPE", "Type1");
       15     content.put("TARGET_ATTR", "tgtAttr"); // if TARGET_ATTR is not specified, a default one will be assigned
       16     content.put("TARGET_ID_TYPE", "tgtType");
       17   
       18     Message msg = new Message(msgId , sender, receiver, msgType , content);
       19     List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
       20     if (!response.isEmpty()) {
       21         Map responseContent = (Map)response.getContent();
       22         boolean succ = (Boolean) responseContent.get("SUCCESS");
       23         String report = (String) responseContent.get("REPORT");
       24         String tgtAttr= (String) responseContent.get("TARGET_ATTR");
       25         if (succ) {
       26             // successfully mapped
       27             // report contains statistics
       28         } else {
       29             // failed
       30             // report contains error message
       31         }
       32     } else {
       33         // the ID mapping services are unavailable
       34     }
       35 
     

4. ID mapping dialog request: Request to bring out the ID mapping main dialog

   •    1   #!java
        2     String sender = pluginName;
        3     String receiver = "CyThesaurus";
        4     String msgType = "MAPPING_DIALOG"; // request for ID mapping main dialog
        5     String msgId = receiver + System.currentTimeMillis();
        6     Message msg = new Message(msgId , sender, receiver, msgType , null);
        7     List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
        8     if (!response.isEmpty()) {
        9         Map content = (Map)response.get(0).getContent();
       10         boolean succ = (Boolean) content.get("SUCCESS");
       11         if (succ) {
       12             // ID mapping was performed successfully
       13         } else {
       14             // ID mapping was not performed or failed
       15         }
       16     } else {
       17         // the ID mapping services are unavailable
       18     }
       19 
     

5. ID mapping source config dialog request: Request to bring out the ID mapping source configuration dialog

   •    1   #!java
        2     String sender = pluginName;
        3     String receiver = "CyThesaurus";
        4     String msgType = "MAPPING_SRC_CONFIG_DIALOG"; // request for ID mapping source configuration dialog
        5     String msgId = receiver + System.currentTimeMillis();
        6     Message msg = new Message(msgId , sender, receiver, msgType , null);
        7     List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
        8     if (!response.isEmpty()) {
        9         Map content = (Map)response.get(0).getContent();
       10         boolean succ = (Boolean) content.get("SUCCESS");
       11         if (succ) {
       12             // ID mapping sources were configured successfully
       13         } else {
       14             // ID mapping sources were not configured or failed
       15         }
       16     } else {
       17         // the ID mapping services are unavailable
       18     }
       19 
     

6. ID mapping supported ID types fetching request: Request to fetch the supported source and target ID types

   •    1   #!java
        2     String sender = pluginName;
        3     String receiver = "CyThesaurus";
        4     String msgType = "REQUEST_SUPPORTED_ID_TYPE"; // request for fetching supported ID types
        5     String msgId = receiver + System.currentTimeMillis();
        6     Message msg = new Message(msgId , sender, receiver, msgType , null);
        7     List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
        8     if (!response.isEmpty()) {
        9         Map content = (Map)response.get(0).getContent();
       10         boolean succ = (Boolean) content.get("SUCCESS");
       11         String report = (String) content.get("REPORT");
       12         if (succ) {
       13             // successfully fetched
       14             // report contains statistics
       15 
       16             String[] supportedSrcIDTypes = (String[]) content.get("SRC_ID_TYPE");
       17             String[] supportedTgtIDTypes = (String[]) content.get("TGT_ID_TYPE");
       18             // do more things here ...
       19         } else {
       20             // failed
       21             // report contains error message
       22         }
       23     } else {
       24         // the ID mapping services are unavailable
       25     }
       26 
     

Demo plugin to consume ID mapping services

• A demo plugin, who consumes ID mapping services provided by CyThesaurus, is available for downloading (CyThesaurusServiceTester.jar, TestCyThesurrusService.java).

• To run the demo plugin, place both CyThesaurus.jar and CyThesaurusServiceTester.jar in the plugin folder of Cytoscape, then start Cytoscape. You will see a menu of Test CyThesaurus Service in the Plugins menu. Click on the sub menus to request different services.

• To request ID mapping service example, you need to import the falFiltered.sif and load the BioMart ID Mapping Service with the dataset of Saccharomyces cerevisiae genes (SGD1.01). You can achieve this by going through Webservice-based identifier mapping tutorial.