Problem using customization in BINGO

Question

[m_02]

Hi all,

I am using Bingo to perform GO-based functional analysis of non-model interactomes.I am working on non-model organism; I have prepared my own custom file for annotation and have downloaded ontology file(go.obo) from gene ontology.

Problem occurs when I run BINGO, the following message appears:

WARNING: Some category labels in the annotation file are not defined in the ontology. Please check the compatibility of these files. For now, these labels will be ignored and calculations will proceed.

I would like to know is this warning message okay or is there something that I am doing wrong.

Annotation file is as follows:

(species=Brugia malayi)(type=Consortium)(curator=GO)
Bm1_55385    = 0005622
Bm1_55385    = 0044444
Bm1_55385    = 0044464
Bm1_04620    = 0043229
Bm1_04620    = 0044444
Bm1_04620    = 0044464
Bm1_41245    = 0030529
Bm1_47775    = 0005622
Bm1_47775    = 0044464
Bm1_28975    = 0005622
Bm1_28975    = 0044464
Bm1_16700    = 0005622
Bm1_16700    = 0032991
Bm1_03855    = 0016020

Thanks in advance

Answer 1

[xanderpico]

I believe it is saying that some of the GO term values you have in your annotation files (e.g., 0005622) are not found in the go.obo file. The key to whether this is a major issue or not is knowing how many of them aren't found :) So, if it's just a a few, then it's ignorable. If none of them are found, then this warning is a way of letting you know that either the annotation or the obo file is not correct.

Can you surmize from your results whether it is a few or all? For example, do you get some enrichment results or none at all?