CyThesaurus_Plugin/ID_Mapping_Examples

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 "ID Mapping Resources Configuration" 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 "ID Mapping Resources Configuration" 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 "ID Mapping Resources Configuration" 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 "ID Mapping Resources Configuration" 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.

RDB-based identifier mapping

PGDB based

1. Install MetScape plugin

2. Start MetScape => Build Compound Reaction Network => Show Pathway => Select a pathway, e.g. TCA Cycle, and draw it.

3. Download http://www.bridgedb.org/data/gene_database/metabolites_081205.pgdb

4. Start CyThesaurus => ID Mapping Resources Configuration => click Databases => Select the pgdb file you just download.

5. At the CyThesarus main dialog, select the compound reaction network you built by MetScape

6. Select "Kegg Compound" as the source ID type for "ID"
7. Select atarget ID type, e.g., ChEBI
8. Click "OK" and wait, close the dialog
9. In the Data Panel, display the new attribute which was just created.