GOChase

Every error that has a beginning has an end.
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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

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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. 

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GOChase-History
Enter a list of GO IDs

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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.  
            

            

            
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 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. 
        

        

        
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 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:

			
				Search field:

			

				
            

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