GO-Slim

Introduction

GO-Slim is a reduced version of the Gene Ontology that contains a selected number of relevant nodes.
GO slims are cut-down versions of the Gene Ontologies that contain a subset of the GO terms. GO slims summarise a set of GO annotations from a genome, microarray, or cDNA collection to a simpler functional schema.

OmicsBox offers the possibility to run GO slim on the data using existing files from the Gene Ontology webpage or provide customised GO Slim files. GO-Slim operates on the annotated functional annotation project, reducing its GO terms to the selected subset.

For more information please visit Gene Ontology page.

Run GO-Slim

The GO Slim feature can be found in the Side Panel of a Functional Annotation Project under Functional Analysis → GO-Slim.

GO Slim Configuration

Different GO-Slims are available which are adapted to specific organisms. OmicsBox supports the following GO-Slim mappings: General, Plant, Yeast, GOA (GO-Association) and TAIR.

• Obo File from GO-Website

• GO-Slim file: Choose the GO slim to use. The file will be directly downloaded from the Gene Ontology webpage.

• Custom Obo File

• Custom GO-Slim file: Browse for the GO slim file to use.

Results

Successful GO Slim for each query sequence will result in a color change for that sequence from blue to yellow at the Main Sequence Table, and only the GO slim GOs will remain in the GO IDs column.

Use the Remove GO-Slim option to return to the original annotations.

OmicsBox Engine

This tool can be run from the command line via the OmicsBox Engine.

Command: omicsbox goslim [options]

Inputs

Parameters

Parameter relationships

Global options (--local-folder, --cloud-folder, --output-format, --config, --detach, --verbose, …) are shared by every Engine tool and are not repeated here — see the OmicsBox Engine reference.