Alternate id in obo file

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Alternate id in obo file

Chen Yian
  Hi all,

In the specification of OBO file format, there is an option tag 'alt_id'
for alternate id.
The OBO parser seems to ignore these tags, and the id will not be found
in database.

New annotations may prevent using these alternate ids,
but sometimes, some old annotation may associate with them.

Any suggestion about how to deal with those ids?

Chen




_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Alternate id in obo file

Richard Smith
Hi Chen,
We can add the ids as synonyms for OntologyTerm, which would mean they
were in the database but this doesn't help much.  What we really need
is for any data attached to an alt id to be automatically moved onto
the current id.  We could do this with an IdResolver as we use for
dealing with old gene ids.  Is that what you need?

I'll put in a ticket, hopefully it can get in our next InterMine
release, currently we're aiming for mid/late August.

Cheers,
Richard.




Chen Yian wrote:

>  Hi all,
>
> In the specification of OBO file format, there is an option tag 'alt_id'
> for alternate id.
> The OBO parser seems to ignore these tags, and the id will not be found
> in database.
>
> New annotations may prevent using these alternate ids,
> but sometimes, some old annotation may associate with them.
>
> Any suggestion about how to deal with those ids?
>
> Chen
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Alternate id in obo file

Chen Yian
  Hi Richard,

Thanks for your suggestion.
That makes sense,
mapping the alternate ids to the current ids could help.
Look forward to the next release.

With best wishes,

Chen

(2010/07/22 23:53), Richard Smith wrote:

> Hi Chen,
> We can add the ids as synonyms for OntologyTerm, which would mean they
> were in the database but this doesn't help much.  What we really need
> is for any data attached to an alt id to be automatically moved onto
> the current id.  We could do this with an IdResolver as we use for
> dealing with old gene ids.  Is that what you need?
>
> I'll put in a ticket, hopefully it can get in our next InterMine
> release, currently we're aiming for mid/late August.
>
> Cheers,
> Richard.
>
>
>
>
> Chen Yian wrote:
>>  Hi all,
>>
>> In the specification of OBO file format, there is an option tag
>> 'alt_id' for alternate id.
>> The OBO parser seems to ignore these tags, and the id will not be
>> found in database.
>>
>> New annotations may prevent using these alternate ids,
>> but sometimes, some old annotation may associate with them.
>>
>> Any suggestion about how to deal with those ids?
>>
>> Chen
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev