[ensembl-dev] how to sort the GO objects hierarchically.

[Fiona Cunningham]

Hi Pablo,

I'm glad you are finding the VEP a useful tool. We do already have a
plugin that retrieves Gene Ontology terms associated with
transcripts/translations. You can see all the plugins here:
https://github.com/ensembl-variation/VEP_plugins

Also we welcome contributions from external users, so if you have
written your own plugin then do let us know!
See more info on our blog:
http://www.ensembl.info/blog/2013/08/07/announcing-ensembl-ecode/

http://www.ensembl.info/ecode/
Fiona

-------------------------------------------------------------------------------------------------
Fiona Cunningham, Variation Annotation Coordinator
Ensembl project, Ensembl Variation Project Leader.
European Bioinformatics Institute (EMBL-EBI)
Genome Campus, Hinxton,  CB10 1SD, UK
www.ensembl.org || www.lrg-sequence.org || t: +44 1223 494612


On 1 April 2014 06:21, pmg <pablo.marin at uv.es> wrote:
> Thanks Kieron,
>
> I know that Ensembl is not necessarily the best codebase to be working with the Gene Ontology but as Ensembl is getting better and better helping to report genomic variation with the VEP, has a strong codebase for functional genomics and large experience working with data stored as tree/graph, I was wondering if someone had implemented a VEP pluging or a misc-scripts demo for the API tutorials covering this topic. If not, I just let it open for your consideration the implementation of such a script that would be very useful for the community. It would help when reporting the result of WES or GWAS and when trying to prioritize SNPs by gene function in a 'quick and dirty way'.
>
> P.S.:
> By the way, where are now located the "ensembl/misc-scripts/ontology/scripts/" in the git repo https://github.com/Ensembl/ensembl/tree/release/75/misc-scripts/ontology there is only the README that mention this scripts folder and the SQL folder but not the scripts.
>
> Regards
>
> P.
>
>
> On 31Mar, 2014, at 5:04 PM, Kieron Taylor wrote:
>
>> Dear Pablo,
>>
>> Ensembl is not necessarily the best codebase to be working with the Gene Ontology. We do not have exactly the code that you asking for. That said, the object Bio::EnsEMBL::DBSQL::OntologyTermAdaptor is able to fetch some of the information needed to build the tree you want.
>>
>> The adaptor will give you the database interface, but you'll still have to compute your own ordering. You could conceivably build up a linear heritage for each term, by hijacking _fetch_ancestor_chart, then rank them by depth, or else crawl the hierarchy manually.
>>
>> Our Compara team spend a lot more time playing with trees of things, so they might have more insight. You might also be better served by investigating the Ontology community, where more thorough graph-centric tools will exist.
>>
>> Regards,
>>
>> --
>> Kieron Taylor PhD.
>> Ensembl Core team
>> EBI
>>
>>
>> On 31/03/2014 15:11, Pablo Marin Garcia wrote:
>>>
>>> Hello,
>>>
>>> Is there arround in the API or tutorials a method that giving several
>>> GO terms it creates its hierarchical tree? I want to sort and print
>>> hierarchically the GO terms returned for a gene.
>>>
>>> Could anyone share code for doing that?
>>>
>>> Pablo
>>>
>>>
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>>
>>
>
> =============================================================
> Pablo Marin-Garcia, PhD
> UNIDAD DE GENOTIPADO Y DIAGNOSTICO GENETICO
> FUNDACIÓN INVESTIGACIÓN CLÍNICO DE VALENCIA-INCLIVA
> Avda. Menéndez Pelayo 4 accesorio
> 46010 VALENCIA
> SPAIN
>
> TELF. 96 197 35 19
> FAX.  96 197 35 40
> e-mail: pablo.marin at uv.es
> http://scholar.google.es/citations?user=7eQG2B8AAAAJ&hl=en
> http://pablomarin-garcia.blogspot.com.es
>
>
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