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 1. Right click on node "Web Services" and click "Add an ID mapping webservice (BioMart)..."
 1. Choose a database as "ENSEMBL 55 GENES (SANGER UK)" 		 1. Click on the node "Web Services"
 1. Choose web service type as "BioMart web service"
 1. Choose a mart/database as "ENSEMBL 55 GENES (SANGER UK)"
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 1. Select "Ensembl Gene ID(s) (ensembl_gene_id)" as the source ID type for attribute "ID"
 1. Select a target ID type, e.g., "EMBL (Genbank) ID (embl)" 		 1. Select "Ensembl Gene ID" as the source ID type for attribute "ID"
 1. Select a target ID type, e.g., "EMBL (Genbank) ID"
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=== PICR based ===
 1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif
 1. From menu: Plugin => !CyThesaurus plugin
 1. Click "Configure sources of ID mapping" at bottom left size of the dialog.
 1. Click on the node "Web Services"
 1. Choose web service type as "PICR web service"
 1. click "OK" and wait.
 1. Select "ENSEMBL_S_CEREVISIAE" as the source ID type for attribute "ID"
 1. Select a target ID type, e.g., "REFSEQ"
 1. Click "OK" and wait, close the dialog
 1. In the Data Panel, display the new attribute which was just created.
=== Synergizer based ===
 1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif
 1. From menu: Plugin => !CyThesaurus plugin
 1. Click "Configure sources of ID mapping" at bottom left size of the dialog.
 1. Click on the node "Web Services"
 1. Choose web service type as Synergizer
 1. Choose a authority as "ensembl"
 1. Choose a species as "Saccharomyces cerevisiae"
 1. click "OK" and wait.
 1. Select "ensembl_gene_id" as the source ID type for attribute "ID"
 1. Select a target ID type, e.g., "ensembl_gene_id"
 1. Click "OK" and wait, close the dialog
 1. In the Data Panel, display the new attribute which was just created.

Contents

  1. File-based identifier mapping
    1. Tab-delimited-text-file based
  2. Webservice-based identifier mapping
    1. BioMart based
    2. PICR based
    3. Synergizer based

File-based identifier mapping

Tab-delimited-text-file based

  1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif

  2. From menu: Plugin => CyThesaurus plugin

  3. Click "Configure sources of ID mapping" at bottom left size of the dialog.
  4. Right click on node "Local/remote Files" and click "Add an ID mapping file..."

  5. Select "Remote/URL" => input http://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt => click "Retrieve" => click "OK" and wait and Click "OK".

  6. Select "Ensembl Gene ID" as the source ID type for attribute "ID"
  7. Click "OK" and wait and Click "OK"
  8. In the Data Panel, display the new attribute which was just created

Webservice-based identifier mapping

BioMart based

  1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif

  2. From menu: Plugin => CyThesaurus plugin

  3. Click "Configure sources of ID mapping" at bottom left size of the dialog.
  4. Click on the node "Web Services"

  5. Choose web service type as "BioMart web service"

  6. Choose a mart/database as "ENSEMBL 55 GENES (SANGER UK)"
  7. Choose a dataset as "Saccharomyces cerevisiae genes (SGD1.01)"
  8. click "OK" and wait.
  9. Select "Ensembl Gene ID" as the source ID type for attribute "ID"
  10. Select a target ID type, e.g., "EMBL (Genbank) ID"
  11. Click "OK" and wait, close the dialog
  12. In the Data Panel, display the new attribute which was just created.

PICR based

  1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif

  2. From menu: Plugin => CyThesaurus plugin

  3. Click "Configure sources of ID mapping" at bottom left size of the dialog.
  4. Click on the node "Web Services"
  5. Choose web service type as "PICR web service"
  6. click "OK" and wait.
  7. Select "ENSEMBL_S_CEREVISIAE" as the source ID type for attribute "ID"
  8. Select a target ID type, e.g., "REFSEQ"
  9. Click "OK" and wait, close the dialog
  10. In the Data Panel, display the new attribute which was just created.

Synergizer based

  1. From menu: File => Import => Network (multiple file types)... => Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif

  2. From menu: Plugin => CyThesaurus plugin

  3. Click "Configure sources of ID mapping" at bottom left size of the dialog.
  4. Click on the node "Web Services"
  5. Choose web service type as Synergizer
  6. Choose a authority as "ensembl"
  7. Choose a species as "Saccharomyces cerevisiae"
  8. click "OK" and wait.
  9. Select "ensembl_gene_id" as the source ID type for attribute "ID"
  10. Select a target ID type, e.g., "ensembl_gene_id"
  11. Click "OK" and wait, close the dialog
  12. In the Data Panel, display the new attribute which was just created.

CyThesaurus_Plugin/ID_Mapping_Examples (last edited 2009-09-03 23:38:04 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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