Guidelines for electronic annotation methods: Difference between revisions

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Annotations made using electronic annotation methods have the Inferred from Electronic Annotation [http://www.geneontology.org/GO.evidence.shtml#iea IEA] evidence code.
Annotations made using electronic annotation methods have the Inferred from Electronic Annotation [http://www.geneontology.org/GO.evidence.shtml#iea IEA] evidence code.


==Types of electronic annotation==
==Types of electronic annotation used by the GO Consortium==


===Mappings used by the GO Consortium===
===Mappings to controlled vocabularies===
One of the primary methods of generating electronic annotations is to manually map GO terms to corresponding concepts in the controlled vocabularies used by the UniProt Knowledgebase or other external resources.  
One of the primary methods of generating electronic annotations is to manually map GO terms to corresponding concepts in the controlled vocabularies used by the UniProt Knowledgebase or other external resources.  
The mappings that are currently used by the GO Consortium to produce annotations are:
The mappings that are currently used by the GO Consortium to produce annotations are:

Revision as of 08:38, 28 July 2010

Electronic GO annotation

Electronic annotation is the process of assigning GO terms to gene products using automated methods. This process can rapidly produce millions of annotations in a very short period of time. The GO terms used for electronic annotation tend to be higher-level and, as such, less detailed than the terms used for manual annotation. It is possible to use certain electronic annotation methods if you have a new genome sequence to annotate, or a microarray with many thousands of sequences. See Using electronic annotation methods to map GO annotation to datasets

Annotations made using electronic annotation methods have the Inferred from Electronic Annotation IEA evidence code.

Types of electronic annotation used by the GO Consortium

Mappings to controlled vocabularies

One of the primary methods of generating electronic annotations is to manually map GO terms to corresponding concepts in the controlled vocabularies used by the UniProt Knowledgebase or other external resources. The mappings that are currently used by the GO Consortium to produce annotations are:

Projection of annotations between orthologous gene products

This method uses orthology data from Ensembl Compara to project GO annotations from a source species onto one or more target species.

Using electronic annotation methods to map GO annotation to datasets

Mapping files consist of entities from external databases indexed to identical, similar or related GO terms. Various mapping files have been created which can be used to provide novel sequences, ESTs, genomes sequences, microarray datasets or peptide sequences with GO annotation.

List of GO mappings to external vocabularies.

One of the most common mappings used to apply electronic GO annotation to user sequences is InterPro2GO.

InterPro

It is possible to assign electronic GO annotation to your sequences based on InterPro domains. For example if your sequence has a DNA binding domain then it would be appropriate to electronically annotate it to the DNA binding function term. For more information on InterPro mapping please see the InterProScan information

InterProScan tool

Using sequence similarity to provide GO annotation to datasets

You can also provide your sequences with annotations by BLASTing them against manually annotated sequences and transferring the GO annotations across to your sequence. Since the originating GO annotation is experimentally derived, the annotation transferred to your sequences could have the Inferred from Sequence or Structural Similarity ISS evidence code.

Two tools which can assist you with this are;

AmiGO BLAST

Blast2GO

Both of these tools allow you to choose the BLAST parameters, the values of which will depend on your individual requirements.