Error: Could not look up this identifier in the identifier mapping database

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Marloes Jonkhout

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Jun 22, 2017, 5:25:53 AM6/22/17
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Hello,

I have RNA-seq data from mice that I want to import in Pathvisio. The gene ID's in the file are given as ENS ID's. However, when importing, I constantly get the same Error: Could not look up this identifier in the identifier mapping database.

Used Gene database: Mm_Derby_Ensembl_85.bridge
Used pathway to import data in: Mm_TNF-alpha_NF-kB_Signaling_Pathway_WP246/-69201.gpml

I have the following data in my import file:
Ensembl ID
System Code (En)
LogFC
Adjusted P-value
Gene_name

In another (old) post, I found that emptying the Appdata folder for Pathvisio should work, but it unfortunately didn't work for me. I also tried Pathvisio with Java7 and 8, there is no difference for me.

Does someone know the trick to make it work? Maybe I'm just doing something completely wrong

Martina Summer-Kutmon

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Jun 22, 2017, 5:55:15 AM6/22/17
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Dear Marloes,

Can you send me a a few lines of your dataset, so I can try it out? 
When you import the data, you need to select the database (system code) - did you maybe choose "Ensembl Mouse"? It's important that you only use "Ensembl" because that's the datasource name used in the mapping database. 

Best regards,
Tina

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Marloes Jonkhout

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Jun 22, 2017, 6:04:13 AM6/22/17
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Dear Tina,

I tried both: Ensembl Mouse and Ensembl. Unfortunately, they didn't work. I'll send you the lines of the set by answering the e-mail you just send me.

Kind regards,
Marloes

Op donderdag 22 juni 2017 11:55:15 UTC+2 schreef Martina Kutmon:
Dear Marloes,

Can you send me a a few lines of your dataset, so I can try it out? 
When you import the data, you need to select the database (system code) - did you maybe choose "Ensembl Mouse"? It's important that you only use "Ensembl" because that's the datasource name used in the mapping database. 

Best regards,
Tina
On Thu, Jun 22, 2017 at 11:25 AM, Marloes Jonkhout <marloes....@gmail.com> wrote:
Hello,

I have RNA-seq data from mice that I want to import in Pathvisio. The gene ID's in the file are given as ENS ID's. However, when importing, I constantly get the same Error: Could not look up this identifier in the identifier mapping database.

Used Gene database: Mm_Derby_Ensembl_85.bridge
Used pathway to import data in: Mm_TNF-alpha_NF-kB_Signaling_Pathway_WP246/-69201.gpml

I have the following data in my import file:
Ensembl ID
System Code (En)
LogFC
Adjusted P-value
Gene_name

In another (old) post, I found that emptying the Appdata folder for Pathvisio should work, but it unfortunately didn't work for me. I also tried Pathvisio with Java7 and 8, there is no difference for me.

Does someone know the trick to make it work? Maybe I'm just doing something completely wrong

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Anders Riutta

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Jun 22, 2017, 4:11:43 PM6/22/17
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The BridgeDb webservice was down for awhile yesterday. Could that have anything to do with problem, or are the mapping databases for PathVisio independent of the webservice?

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Martina Summer-Kutmon, PhD
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Marloes Jonkhout

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Jun 23, 2017, 7:01:17 AM6/23/17
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Dear Anders,

I don't know. The data import still has the same result today: error. Is there maybe some kind of additional plugin that I need to install?

Op donderdag 22 juni 2017 22:11:43 UTC+2 schreef Anders Riutta at Gladstone:
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Martina Summer-Kutmon, PhD
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Martina Summer-Kutmon

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Jun 23, 2017, 10:13:25 AM6/23/17
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Dear Marloes,

No, the BridgeDb webservice is unrelated (PathVisio has local databases). I had a look at your example data. I think the problem is with the identifiers in your file.
As an example:
The identifier in your dataset is ENSMUSG00000000386.14 --> what does the .14 add here? The identifier in Ensembl is ENSMUSG00000000386. The identifier with ".14" does not exist.

Best, Tina


Dear Anders,

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Marloes Jonkhout

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Jun 23, 2017, 11:39:06 AM6/23/17
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Dear Tina,

Thank you, this indeed solved my problem! The .14 apparently doesn't mean anything.

Best,
Marloes

Op vrijdag 23 juni 2017 16:13:25 UTC+2 schreef Martina Kutmon:
Dear Anders,

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