GOChase

Every error that has a beginning has an end.

GOChase: correcting errors from gene ontology-based annotations for gene products

Yu Rang Park, Chan Hee Park, Ju Han Kim
Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea

The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes,cellular components, and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based highlevel analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.


Availability: http://www.snubi.org/software/GOChase/
Contact: juhan@snu.ac.kr

Bioinformatics 2005 Mar;21(6):829-31

GOChase:

The Gene Ontology (GO) is a rapidly growing hierarchy of controlled vocabularies for describing biological processes, cellular components, and molecular functions. 

Many databases of gene products are annotated with GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. 

Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. 

GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

(1) GOChase-History resolves the whole modification history of GO IDs. 

(2) GOChase-Correct highlights a merged term and redirects it to the correct target term into which the merged term was merged. For a discarded (or obsolete) GO term, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGo and QuickGO to fix the broken hyperlinks. 

(3) A whole database (such as LocusLink) as a flat file can be input to GOChase, reporting the annotation errors and GOChase corrections. 

(4) When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. 

GOChase-History
Enter a list of GO IDs

Example GO IDs:
GO:0005856
GO:0005576
GO:0007327
GO:0046777
GO:0016021
GO:0006951
GO:0006489

		
GOChase-Correct
Enter a list of tab-delimited <id>-<GO ID> pairs.

Example input: 
ABCA1	GO:0004002
ABCA1	GO:0008509
ABCA1	GO:0006832
SERPINH1	GO:0006951
DMD	GO:0000157
DMD	GO:0007327
DMD	GO:0007517
DMD	GO:0005856
Correct errors in a flat file
Enter a list of tab-delimited <id>-<GO ID> pairs in a flat-file format.

Example input file:

Sample flat file(subset of loc2go_20031130)

Find gene products with GO-annotations
Examples

GO IDs

GO:0004002
GO:0000157
GO:0007327
GO:0007517
GO:0005856

GO Terms

microtubule-based process
regulation of growth rate
cytoskeleton
pheromone catabolism
response to heat shock

Gene Description

breast cancer
heat shock protein 
microtubule-associated
ATP binding
molecule transport

Datasource:
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