GO evidence

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GO evidence

Dr Intikhab Alam
Hi,

How does the Gene Ontology displayer work on the gene report page? Does Gene Ontology Evidence code read by the source "go" or we have provide it when we assign GO terms to Genes?

I assign GO terms to Gens from Interproscan results and read the gene_ontology.obo file using go source defined in the project xml. I can list columns with GO ontology and the list function shows GO enrichment as well. The gene report page Gene Ontology displayer always says:

Gene Ontology

biological process
No terms in this category.
molecular function
No terms in this category.
cellular component
No terms in this category.

Intikhab


PS. In the new release of intermine, FASTA, GFF3 and some other converters are not working.


-- 
--
Intikhab Alam, PhD

Research Scientist
Computational Bioscience Research Centre (CBRC), Building #2, Office #4332
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, KSA
W: http://www.kaust.edu.sa
T +966 (0) 2 808-2423  F +966 (2) 802 0127


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Re: GO evidence

Julie Sullivan
Hi Intikhab

The evidence code is located in the gene annotation file, so you would have to
either provide these data when you assign GO terms to genes or remove evidence
code from the GO displayer.

The FASTA and GFF3 converters haven't been changed in a while. Let me know what
sort of errors are occurring and I'll take a look.

Julie

On 13/11/12 09:04, Dr Intikhab Alam wrote:
> Hi,
>
> How does the Gene Ontology displayer work on the gene report page? Does Gene Ontology Evidence code read by the source "go" or we have provide it when we assign GO terms to Genes?
>
> I assign GO terms to Gens from Interproscan results and read the gene_ontology.obo file using go source defined in the project xml. I can list columns with GO ontology and the list function shows

GO enrichment as well. The gene report page Gene Ontology displayer always says:

>
> Gene Ontology
> biological process
> No terms in this category.
> molecular function
> No terms in this category.
> cellular component
> No terms in this category.
>
> Intikhab
>
>
> PS. In the new release of intermine, FASTA, GFF3 and some other converters are not working.
>
>
> --
> --
> Intikhab Alam, PhD
>
> Research Scientist
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4332
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, KSA
> W: http://www.kaust.edu.sa
> T +966 (0) 2 808-2423  F +966 (2) 802 0127
>
> ________________________________
> This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
>
>
>
>
> _______________________________________________
> 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