Guidelines for electronic annotation methods: Difference between revisions

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[[Category:Annotation Guidelines]]
==Electronic GO annotation==
==Electronic GO annotation==


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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 [http://wiki.geneontology.org/index.php/Guidelines_for_electronic_annotation_methods#Using_electronic_annotation_methods_to_map_GO_annotation_to_datasets Using electronic annotation methods to map GO annotation to datasets]
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 [http://wiki.geneontology.org/index.php/Guidelines_for_electronic_annotation_methods#Using_electronic_annotation_methods_to_map_GO_annotation_to_datasets Using electronic annotation methods to map GO annotation to datasets]


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


===Mapping from controlled vocabularies===
==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.  
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 controlled vocabularies that are currently mapped are:
The mappings that are currently used by the GO Consortium to produce annotations are:
*[[Swiss-Prot_keywords_SPKW2GO|Swiss-Prot keywords (SPKW2GO)]]
*[[Swiss-Prot_keywords_SPKW2GO|Swiss-Prot keywords (SPKW2GO)]]
*[[Subcellular_locations_SPSL2GO|Subcellular locations (SPSL2GO)]]
*[[Subcellular_locations_SPSL2GO|Subcellular locations (SPSL2GO)]]
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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]]


==Using electronic annotation methods to map GO annotation to datasets==
==Using electronic annotation methods to map GO annotation to datasets==
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[http://www.geneontology.org/GO.indices.shtml List of GO mappings to external vocabularies].
[http://www.geneontology.org/GO.indices.shtml List of GO mappings to external vocabularies].


Two of the most common methods of applying electronic GO annotation to user sequences are InterPro2GO and BLAST.
One of the most common mappings used to apply electronic GO annotation to user sequences is InterPro2GO.


===InterPro===
===InterPro===
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[http://www.ebi.ac.uk/Tools/InterProScan/ InterProScan tool]
[http://www.ebi.ac.uk/Tools/InterProScan/ InterProScan tool]


===BLAST===
==Using sequence similarity to provide GO annotation to datasets==


You can also make electronic annotations by BLASTing your sequence against manually annotated sequences and transferring the GO annotations across to your sequence. Two tools which can assist you with this are;
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 [http://www.geneontology.org/GO.evidence.shtml#iss ISS] evidence code.
 
Two tools which can assist you with this are;


[http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi AmiGO BLAST]
[http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi AmiGO BLAST]
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Both of these tools allow you to choose the BLAST parameters, the values of which will depend on your individual requirements.
Both of these tools allow you to choose the BLAST parameters, the values of which will depend on your individual requirements.
== COMMENTS ==
Perhaps the name for this page should change from electronic -> automatic annotation methods? As then you could include the f2p inferences - these won't have the IEA evidence tag (which seems to be implied by the 'electronic' wording of the page title), but are applied automatically from the f2p links in the GO file and it would be nice to have an explanation of the process here, especially as no GO_REF will be associated with the annotation set. I've drafted an explanation of this annotation method:
GOC Inferred Annotations
Annotations automatically generated using the Molecular Function->Biological Process inter-ontology relationships present in the GO OBO  v1.2 format. As many GO users do not currently reason over these relationships, a set of inferred annotations are being generated. Such GO annotations are produced when an annotation has been made (either manually or electronically) to a Molecular Function term that, either directly or via one of its parent terms, has an relationship to a Biological Process term, and where this Process term (or one of its children) has not already been used in the annotation set for the same gene product identifier. This inferred annotation set applies the same gene product identifier, reference and evidence code as the asserted function annotation and are generated from all sources of GO annotations, with only 'NOT'-qualified annotations being excluded.
As an example, you can see an inter-ontology relationship exists to indicate 'GTPase activity' is a part_of the 'GTP catabolic process', as displayed here: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003924#term=ancchart .
[[User:Edimmer|Edimmer]]

Latest revision as of 12:04, 13 April 2019

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.


COMMENTS

Perhaps the name for this page should change from electronic -> automatic annotation methods? As then you could include the f2p inferences - these won't have the IEA evidence tag (which seems to be implied by the 'electronic' wording of the page title), but are applied automatically from the f2p links in the GO file and it would be nice to have an explanation of the process here, especially as no GO_REF will be associated with the annotation set. I've drafted an explanation of this annotation method:

GOC Inferred Annotations

Annotations automatically generated using the Molecular Function->Biological Process inter-ontology relationships present in the GO OBO v1.2 format. As many GO users do not currently reason over these relationships, a set of inferred annotations are being generated. Such GO annotations are produced when an annotation has been made (either manually or electronically) to a Molecular Function term that, either directly or via one of its parent terms, has an relationship to a Biological Process term, and where this Process term (or one of its children) has not already been used in the annotation set for the same gene product identifier. This inferred annotation set applies the same gene product identifier, reference and evidence code as the asserted function annotation and are generated from all sources of GO annotations, with only 'NOT'-qualified annotations being excluded.

As an example, you can see an inter-ontology relationship exists to indicate 'GTPase activity' is a part_of the 'GTP catabolic process', as displayed here: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003924#term=ancchart . Edimmer