[ensembl-dev] ids from older versions of Ensembl.

[Nick Langridge]

Hello again,

After talking to my colleagues, I can give you an update on this. The ID 
history converter tool is enabled for EG Bacteria, however not all 
historical IDs are mapped:
"For protein coding genes, we use common identifiers (protein_ids) to do 
the mapping from old to new. In this case, it appears to be an RNA gene 
which was predicted in the old version by us running a third party 
program. We no longer do this with the new system, where RNA genes come 
from ENA annotation. This means there are no common identifiers we can 
use, so we have not mapped these over. It might be possible to do this 
mapping using sequence idenitiy or genome location overlap, but this 
isn't something we've done."

If you have other IDs you wish to try looking up, here are some brief 
instructions for using the ID history converter in EG Bacteria (we plan 
to make this a little easier in future versions):

1. Visit a gene or location page for the species you are interested in, 
e.g. 
http://bacteria.ensembl.org/escherichia_coli_str_k_12_substr_mg1655/Location/View?r=Chromosome:1130661-1131065;time=1376564739066.066

2. Click the 'Add your data' button in the left-hand navigation to open 
the configuration panel.

3. Choose  'ID History Converter'

4. Enter an ID (e.g. EBESCG00000000900), click Next, then choose a format.

I hope this helps.

Best regards,
Nick



On 14/08/2013 15:32, Nick Langridge wrote:
> Hi Adam,
>
> This should be possible using the ID history converter tool, however 
> the tool is not currently enabled for Ensembl Bacteria.
> I will look into this and get back to you.
>
> Best regards,
> Nick
>
> On 14/08/2013 14:07, Adam Witney wrote:
>>
>> Hi,
>>
>> Is there any way in Ensembl Bacteria to map older IDs to new IDs. 
>> e.g. I have some genes labelled with IDs like EBSTRG00000063753, but 
>> these don't find anything with the search field
>>
>> Thanks
>>
>> Adam
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: 
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>