Guidelines for electronic annotation methods: Difference between revisions

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===Projection of annotations between orthologous gene products===
===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.  
This method uses orthology data from Ensembl Compara to project GO annotations from a source species onto one or more target species.  
[[Ensembl_Compara|Ensembl Compara orthology electronic annotation method]]


*[[Ensembl_Compara|Ensembl Compara orthology electronic annotation method]]


===Old documentation===
===Old documentation===

Revision as of 09:34, 21 June 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.

Types of electronic annotation

Mapping from 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. The controlled vocabularies that are currently mapped 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.

Old documentation

Taken from http://www.geneontology.org/GO.annotation.SOP.shtml

Electronic annotation is very quick and produces large amounts of less detailed annotation very quickly. Electronic annotations are rarely wrong, but tend to be less detailed. For example, electronic annotation is likely to tell you which of your genes are transcription factors but unlikely to tell you in great detail what process the gene controls. You may like to use this method if you have a new genome sequence to annotate, or a microarray with many thousands of sequences.

Diagram giving overview of electronic annotation

[File:diag-iea-overview.png]

This diagram illustrates some of the main ways of making electronic annotation. It should be read from the top down. The diagram shows sequences from UniProt having electronic GO annotation assigned by several computational methods. All of these methods involve use of mapping files. For more information on mappings see the information on mappings of GO to other classification systems. InterPro Mapping

In the case of the Interpro mapping it is possible to assign electronic GO annotation to your sequences based on InterPro domains and a number of other criteria. For example if your sequence has a DNA binding domain then it makes sense to electronically annotate it to the DNA binding function term. For more information on InterPro mapping please see the information on InterProScan. UniProt Keyword Mapping

This part of the diagram illustrates how sequences already categorised using the UniProt keyword mapping can have GO annotation automatically applied by transferring via the keyword mapping file. HAMAP

HAMAP is a system that categorizes sequences based on family or subfamily characteristics and is applied to bacterial, archaeal and plastid-encoded proteins. GO annotation can be automatically applied to such sequences using the mapping file between HAMAP and GO. Enzyme Commission

The Enzyme Commission database categories enzymes by the reactions they catalyse. If your sequences are already categories by EC then you can transfer GO annotations using the mapping file of EC to GO categories. Other mappings

These are just a few examples of mapping files that can be used to transfer annotations to your sequence objects. Many other mappings are available, and if there is not a mapping file between GO and your current annotation system, we can assist you in making one. BLAST

You can also make electronic annotations by BLASTing your sequence against manually annotated sequences and transferring the GO annotations across to your sequence. The threshold of similarity in this process is up to you, and depends on your requirements. No similar sequences manually annotated?

If your sequence is similar to other sequences that have been well characterised but not yet annotated from the literature, then one option is to carry out the literature annotation yourself and then transfer by electronic methods.