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

[Adam Witney]

Thanks Nick,

I would be looking to convert IDs for the whole genome. Do you not have 
a mapping file available?

Thanks

Adam

On 15. 8. 2013 15:57, Nick Langridge wrote:
> 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
>>>
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>>
>
>
>
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