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[UNDER CONSTRUCTION] <<TableOfContents(4)>>
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<<TableOfContents(4)>> == Plugin availability ==
 * From plugin manager: in category ''Network and Attribute I/O''.
 * Source code: http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/IDMapping/
 * Tutorial: http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/ID_Mapping_Examples
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==== 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. 		 * 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.
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==== PGDB file ====
 * Gene database schema: http://www.bridgedb.org/wiki/GeneDatabaseLayout
 * Gene databases are available at http://bridgedb.org/data/gene_database/ 		 * PGDB file is supported
  * Gene database schema: http://www.bridgedb.org/wiki/GeneDatabaseLayout
  * Gene databases are available at http://bridgedb.org/data/gene_database/
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==== BioMart web service ====
[[http://www.biomart.org|BioMart]] web service has been utilized to provide ID mapping service in this plugin. 		 * [[http://www.biomart.org|BioMart]] web service has been utilized to provide ID mapping service in this plugin.
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==== BridgeDb web service ====
Being developed. 		 * [[http://www.bridgedb.org|BridgeDb]] web service is being developed.
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==== PICR web service ====
Being developed. 		 * [[http://www.ebi.ac.uk/Tools/picr/|PICR - Protein Identifier Cross-Reference Service]] has been integrated.

 * [[http://llama.med.harvard.edu/synergizer/translate/|Synergizer web service]] has been integrated.
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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 ([[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/IDMapping/lib/cytoscape-plugins-comm.jar|.jar]], [[http://web.missouri.edu/~jg722/GSoC/cytoscape-plugins-comm-javadoc/|javadoc]], [[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/PluginsCommunication/|src]]). The following services are supported.
=== Supported ID mapping services ===
 1. '''Test request''': Test if the services are available.
  {{{
  #!java
    String sender = pluginName;
    String receiver = "CyThesaurus"; // plugin name when passing messages
    String msgType = Message.MSG_TYPE_TEST; // indicate what this message requests for
    String msgId = receiver + System.currentTimeMillis();
    Message msg = new Message(msgId , sender, receiver, msgType , null);
    List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
    if (!response.isEmpty()) {
        // the ID mapping services are available
    }
  }}}
 1. '''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
  {{{
  #!java
    String sender = pluginName;
    String receiver = "CyThesaurus";
    String msgType = "REQUEST_MAPPING"; // request for ID mapping service
    String msgId = receiver + System.currentTimeMillis();
    Map content = new HashMap();
    content.put("NETWORK_ID", new String[]{"net1", "net2"}); // if NETWORK_ID is not specified,
                                        //ID mapping will be performed on all networks in session
    // or content.put("NETWORK_ID", "net1");
    content.put("SOURCE_ATTR", new String[]{"Attr1", "Attr2"});
    // or content.put("SOURCE_ATTR", "ID");
    content.put("SOURCE_ID_TYPE", new String[]{"Type1","Type2"}); // if SOURCE_ID_TYPE is not specified,
                                                          //all supported source id types will be used
    // or content.put("SOURCE_ID_TYPE", "Type1");
    content.put("TARGET_ATTR", "tgtAttr"); // if TARGET_ATTR is not specified, a default one will be assigned
    content.put("TARGET_ID_TYPE", "tgtType");
  
    Message msg = new Message(msgId , sender, receiver, msgType , content);
    List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
    if (!response.isEmpty()) {
        Map responseContent = (Map)response.getContent();
        boolean succ = (Boolean) responseContent.get("SUCCESS");
        String report = (String) responseContent.get("REPORT");
        String tgtAttr= (String) responseContent.get("TARGET_ATTR");
        if (succ) {
            // successfully mapped
            // report contains statistics
        } else {
            // failed
            // report contains error message
        }
    } else {
        // the ID mapping services are unavailable
    }
  }}}
 1. '''ID mapping dialog request''': Request to bring out the ID mapping main dialog
  {{{
  #!java
    String sender = pluginName;
    String receiver = "CyThesaurus";
    String msgType = "MAPPING_DIALOG"; // request for ID mapping main dialog
    String msgId = receiver + System.currentTimeMillis();
    Message msg = new Message(msgId , sender, receiver, msgType , null);
    List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
    if (!response.isEmpty()) {
        Map content = (Map)response.get(0).getContent();
        boolean succ = (Boolean) content.get("SUCCESS");
        if (succ) {
            // ID mapping was performed successfully
        } else {
            // ID mapping was not performed or failed
        }
    } else {
        // the ID mapping services are unavailable
    }
  }}}
 1. '''ID mapping source config dialog request''': Request to bring out the ID mapping source configuration dialog
  {{{
  #!java
    String sender = pluginName;
    String receiver = "CyThesaurus";
    String msgType = "MAPPING_SRC_CONFIG_DIALOG"; // request for ID mapping source configuration dialog
    String msgId = receiver + System.currentTimeMillis();
    Message msg = new Message(msgId , sender, receiver, msgType , null);
    List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
    if (!response.isEmpty()) {
        Map content = (Map)response.get(0).getContent();
        boolean succ = (Boolean) content.get("SUCCESS");
        if (succ) {
            // ID mapping sources were configured successfully
        } else {
            // ID mapping sources were not configured or failed
        }
    } else {
        // the ID mapping services are unavailable
    }
  }}}
 1. '''ID mapping supported ID types fetching request''': Request to fetch the supported source and target ID types
  {{{
  #!java
    String sender = pluginName;
    String receiver = "CyThesaurus";
    String msgType = "REQUEST_SUPPORTED_ID_TYPE"; // request for fetching supported ID types
    String msgId = receiver + System.currentTimeMillis();
    Message msg = new Message(msgId , sender, receiver, msgType , null);
    List<ResponseMessage> response = PluginsCommunicationSupport.sendMessageAndGetResponses(msg);
    if (!response.isEmpty()) {
        Map content = (Map)response.get(0).getContent();
        boolean succ = (Boolean) content.get("SUCCESS");
        String report = (String) content.get("REPORT");
        if (succ) {
            // successfully fetched
            // report contains statistics 		An inter-plugin communication module was developed to support !CyThesaurus plugin providing ID mapping services to other plugins. A inter-plugin communication package cytoscape-plugins-comm was developed. ( [[attachment:cytoscape-plugins-comm.jar]], [[http://web.missouri.edu/~jg722/GSoC/cytoscape-plugins-comm-javadoc/|javadoc]], [[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/PluginsCommunication/|src]]). It is recommended that other plugins, who need to request ID mapping services from !CyThesaurus, include the [[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/IDMappingService/CyThesaurusService.jar|CyThesaurusService]], which wraps up the messages in a class.
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            String[] supportedSrcIDTypes = (String[]) content.get("SRC_ID_TYPE");
            String[] supportedTgtIDTypes = (String[]) content.get("TGT_ID_TYPE");
            // do more things here ...
        } else {
            // failed
            // report contains error message
        }
    } else {
        // the ID mapping services are unavailable
    }
  }}}
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 * To run the demo plugin, place both [[http://web.missouri.edu/~jg722/GSoC/CyThesaurus.jar|CyThesaurus.jar]] and [[attachment: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 run the demo plugin, install !CyThesaurus plugin and place [[attachment: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.
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 * To request the ''ID mapping service example'' request, 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 [[http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/ID_Mapping_Examples#BioMart_based|Webservice-based identifier mapping tutorial]].  * 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 [[http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/ID_Mapping_Examples#BioMart_based|Webservice-based identifier mapping tutorial]].

Contents

  1. Plugin availability
  2. Introduction
  3. Use Cases
  4. Supported ID Mapping Resources
    1. File- based
    2. RDB based
    3. Web service based
  5. Code Base
  6. ID mapping service for other plugin
    1. Demo plugin to consume ID mapping services

Plugin availability

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

Web service based

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. A inter-plugin communication package cytoscape-plugins-comm was developed. ( cytoscape-plugins-comm.jar, javadoc, src). It is recommended that other plugins, who need to request ID mapping services from CyThesaurus, include the CyThesaurusService, which wraps up the messages in a class.

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, install CyThesaurus plugin and place 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.

CyThesaurus_Plugin (last edited 2011-03-29 16:03:58 by asp)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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