[ensembl-dev] Ensembl ID History Converter (IDmapper.pl) API inconsistent with web tool

[Anne Parker]

Hi Lucas

The discrepancy may have arisen because the web tool doesn't currently use the API script but implements the (in theory) same process through the API directly. It may be that the script has been changed since we wrote the web tool, so I will have to investigate that. 

At some point in the future we will be migrating the web tools to a new system that does use the latest version of the API script directly - please watch our blog for announcements!

Hope this helps

Anne


On 29 May 2012, at 19:08, Lucas Swanson wrote:

> Hello,
> 
> I have a large number of old Ensembl gene IDs for which I want to determine the corresponding IDs in the latest release. The Ensembl FAQ pointed me to the ID History converter. However, I am noticing some inconsistencies between the web tool and the downloaded API (which I will need to use since I have more than 30 ids).
> 
> The API version used is 67
> $ echo "ENSG00000164012" | /home/lswanson/ensembl/id_history_converter/IDmapper.pl -s human
> Old stable ID, New stable ID, Release, Mapping score
> ENSG00000164012.1, ENSG00000164012.1, 7, 0
> ENSG00000164012.1, ENSG00000164012.1, 10, 0
> ENSG00000164012.1, ENSG00000164012.1, 14, 0
> ENSG00000164012.1, ENSG00000164012.1, 15, 0
> ENSG00000164012.1, ENSG00000164012.1, 18.2, 0
> ENSG00000164012.1, ENSG00000164012.1, 18.1, 0
> ENSG00000164012.1, ENSG00000164012.1, 21, 0
> ENSG00000164012.1, ENSG00000164012.1, 26, 0
> ENSG00000164012.1, ENSG00000164012.1, 27, 0
> ENSG00000164012.1, ENSG00000164012.2, 38, 0
> ENSG00000164012.2, ENSG00000164012.3, 40, 0.666667
> ENSG00000164012.3, ENSG00000164012.4, 55, 0.586106
> ENSG00000164012.4, ENSG00000164012.5, 56, 0.738542
> ENSG00000164012.5, <retired>, 61, 0
> 
> But when I enter ENSG00000164012 into the web tool, I get the results in the attached screenshot.
> 
> Why does the API not return any mention of "ENSG00000117395", which is what I would like since it is actually still active, while "ENSG00000164012" has been retired?
> 
> Also, I am uncertain about the "Mapping score" column in the API output. What does it represent, and is a higher number better, or is a lower number better?
> 
> ~Thank you,
> Lucas Swanson
> 
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org