GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog - Revision history

Agoesman at 10:37, 30 November 2011

2011-11-30T10:37:16Z

← Older revision		Revision as of 12:37, 30 November 2011
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	close the annotation dialog press the 'Close' button.		close the annotation dialog press the 'Close' button.

	~~attachment~~:~~annotationDialogRegion~~.png		[[File:AnnotationRegion.png\|Screenshot of the Region Annotation Dialog.]]


	== Function Annotation ==		== Function Annotation ==
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	The following fields have already been described for the Region Annotation.		The following fields have already been described for the Region Annotation.

	[[File:~~annotationDialog~~.png]]		[[File:AnnotationFunction.png\|Screenshot of the Function Annotation Dialog.]]

Agoesman at 19:55, 15 November 2011

2011-11-15T19:55:07Z

Agoesman: Created page with "= Annotation Dialog = In this section the manual annotation of a Region using the Web Interface is described. A description of the terms and concepts of the GenDB annotation co..."

2011-10-28T13:29:06Z

Created page with "= Annotation Dialog = In this section the manual annotation of a Region using the Web Interface is described. A description of the terms and concepts of the GenDB annotation co..."

New page

= Annotation Dialog =

In this section the manual annotation of a Region using the Web Interface is
described. A description of the terms and concepts of the GenDB annotation
concept can be found in the [wiki:GenDBWiki/TermsAndConcepts/AnnotationConcepts AnnotationConcepts] of the [wiki:GenDBWiki/TermsAndConcepts Terms and Concepts Section]

Two kinds of annotations do fully characterize a region:

* [#RegionAnnotation a Region Annotation]
* [#FunctionAnnotation a Function Annotation]

[[Anchor(RegionAnnotation)]]
== Region Annotation ==

The following image shows the annotation dialog of the GenDB Web interface.
The first line informs about the region name and - if available - the biological
name of the region. On both sides of this line there are arrows to access the
previous or the following of the current region.

On the left side, the list of functional and regional annotations is located.
The selected annotation is marked in blue and shown on the right side in the
Annotation Detail section. In this case, it is a regional annotation done by the
Critica auto annotator.

In the two drop down menues 'Set regional status to' and 'Set functional status to'
a number of stati for the two different annotation types can be chosen. A completely
annotated coding sequence should have the two stati shown here which is 'finished'
for the regional and 'annotated' for the functional annotation.

Following the date and the annotator (which can be a human or an autoannotator) the
start and the stop position of the region are displayed. These can be changed in the
[wiki:GenDBWiki/WebDocumentation/DialogWindows/RegionEditor Region Editor].

After the description field and the comment field there are the observations that
leaded to the current annotation listed. The following field contains additional
observations that can be added to the list via the buttons 'Show selected ...' to look
at selected observations or 'Add observations...' to add them manually to the list.

The last section shows links for the current annotation. New links can be added in the
field right to the links.

On the bottom and on the top of the Annotation Dialog there are three buttons, respectively.
These have the functions to add a new annotation ('Add new') or accept an annotation (which
means the same as 'Add new' but the regional status is automatically set to 'finished' and
the functional status is automatically set to 'annotated'). To make no changes and just
close the annotation dialog press the 'Close' button.

attachment:annotationDialogRegion.png

[[Anchor(FunctionAnnotation)]]
== Function Annotation ==

Choosing a functional annotation on the left side a number of additional fields occur on
the right side. One additional field is an entry for the Genename for coding regions which
is a biological identifier for the region. A certain gene name should only be given once
for a genome.

Right from the Genename entry there is the possibility to add !GeneOntology numbers as a
functional classification for the gene. More information to each GO number can be accessed
via the links next to the field.

The EC-Number entry can contain one Enzyme Commission number that is a numerical classification
scheme for enzymes. Genes that do not code for enzymes do not get such a number. The EC numbers
can be used for the reconstruction of the metabolic pathways of the organism e.g. in
[wiki:GenDBWiki/WebDocumentation/MainViews/KEGGView KEGG].

In the Gene Product field the gene is shortly characterized. If there is no exact characterization
possible, there are different types of classes available for a gene product. These can be
accessed in the drop down menu below the Gene Product entry and is entered in the entry after
choosing one. Examples are 'hypothetical protein' if no further information is available for
the gene product or 'conserved hypothetical protein' if there is at least one good hit to
a protein in another organism.

The Description field of the functional annotation is a further detailed characterization of
the gene product. It is exported to the EMBL output of the genome. This is not the case
for any entries in the Comment field.

Below the description field there is the check box 'Experimental' which should be clicked if any
of the results of the annotation are verified in the wet lab. Following are entries concerning
the COG (Cluster of orthologous group) functional classification, namely the COG number, COG
funccat ID and COG funccat Description. These fields cannot be edited manually, but only
pressing the button 'Get' on the right. In the upcoming dialog a COG number can be selected and
the entries will be filled.

In the 'Function' field a short description of the function of the gene can be inserted.
A confidence for the complete annotation is also to be entered in the respective drop down field.
There are different confidence stati that can be chosen here. The strongest confidence is
'High confidence in function and specificity' and the weakest is 'Hypothetical protein'.

The following fields have already been described for the [#RegionAnnotation Region Annotation].

[[File:annotationDialog.png]]

← Older revision		Revision as of 21:55, 15 November 2011
Line 2:		Line 2:

	In this section the manual annotation of a Region using the Web Interface is		In this section the manual annotation of a Region using the Web Interface is
	described. A description of the terms and concepts of the GenDB annotation		described. A description of the terms and concepts of the GenDB annotation
	concept can be found in the [~~wiki:~~GenDBWiki/TermsAndConcepts/AnnotationConcepts ~~AnnotationConcepts~~] of the [~~wiki:~~GenDBWiki/TermsAndConcepts Terms and Concepts Section]		concept can be found in the [[GenDBWiki/TermsAndConcepts/AnnotationConcepts\|Annotation Concepts]] of the [[GenDBWiki/TermsAndConcepts\|Terms and Concepts Section]]

	Two kinds of annotations do fully characterize a region:		Two kinds of annotations do fully characterize a region:

	* ~~[#RegionAnnotation a~~ Region Annotation]		* A Region Annotation
	* ~~[#FunctionAnnotation a~~ Function Annotation]		* A Function Annotation

	~~[[Anchor(RegionAnnotation)]]~~
	== Region Annotation ==		== Region Annotation ==

	The following image shows the annotation dialog of the GenDB Web interface.		The following image shows the annotation dialog of the GenDB Web interface.
	The first line informs about the region name and - if available - the biological		The first line informs about the region name and - if available - the biological
	name of the region. On both sides of this line there are arrows to access the		name of the region. On both sides of this line there are arrows to access the
	previous or the following of the current region.		previous or the following of the current region.

	On the left side, the list of functional and regional annotations is located.		On the left side, the list of functional and regional annotations is located.
	The selected annotation is marked in blue and shown on the right side in the		The selected annotation is marked in blue and shown on the right side in the
	Annotation Detail section. In this case, it is a regional annotation done by the		Annotation Detail section. In this case, it is a regional annotation done by the
	Critica auto annotator.		Critica auto annotator.

Line 30:		Line 29:
	Following the date and the annotator (which can be a human or an autoannotator) the		Following the date and the annotator (which can be a human or an autoannotator) the
	start and the stop position of the region are displayed. These can be changed in the		start and the stop position of the region are displayed. These can be changed in the
	[~~wiki:~~GenDBWiki/WebDocumentation/DialogWindows/RegionEditor Region Editor].		[[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor\|Region Editor]].

	After the description field and the comment field there are the observations that		After the description field and the comment field there are the observations that
Line 41:		Line 40:

	On the bottom and on the top of the Annotation Dialog there are three buttons, respectively.		On the bottom and on the top of the Annotation Dialog there are three buttons, respectively.
	These have the functions to add a new annotation ('Add new') or accept an annotation (which		These have the functions to add a new annotation ('Add new') or accept an annotation (which
	means the same as 'Add new' but the regional status is automatically set to 'finished' and		means the same as 'Add new' but the regional status is automatically set to 'finished' and
	the functional status is automatically set to 'annotated'). To make no changes and just		the functional status is automatically set to 'annotated'). To make no changes and just
	close the annotation dialog press the 'Close' button.		close the annotation dialog press the 'Close' button.

	attachment:annotationDialogRegion.png		attachment:annotationDialogRegion.png

	~~[[Anchor(FunctionAnnotation)]]~~
	== Function Annotation ==		== Function Annotation ==

	Choosing a functional annotation on the left side a number of additional fields occur on		Choosing a functional annotation on the left side a number of additional fields occur on
	the right side. One additional field is an entry for the ~~Genename~~ for coding regions which		the right side. One additional field is an entry for the gene name for coding regions which
	is a biological identifier for the region. A certain gene name should only be given once		is a biological identifier for the region. A certain gene name should only be given once
	for a genome.		for a genome.

	Right from the ~~Genename~~ entry there is the possibility to add !GeneOntology numbers as a		Right from the gene name entry there is the possibility to add GeneOntology numbers as a
	functional classification for the gene. More information to each GO number can be accessed		functional classification for the gene. More information to each GO number can be accessed
	via the links next to the field.		via the links next to the field.

	The EC-Number entry can contain one Enzyme Commission number that is a numerical classification		The EC-Number entry can contain one Enzyme Commission number that is a numerical classification
	scheme for enzymes. Genes that do not code for enzymes do not get such a number. The EC numbers		scheme for enzymes. Genes that do not code for enzymes do not get such a number. The EC numbers
	can be used for the reconstruction of the metabolic pathways of the organism e.g. in		can be used for the reconstruction of the metabolic pathways of the organism e.g. in [[GenDBWiki/WebDocumentation/MainViews/KEGGView\|KEGG]].
	[~~wiki:~~GenDBWiki/WebDocumentation/MainViews/KEGGView KEGG].

	In the Gene Product field the gene is shortly characterized. If there is no exact characterization		In the Gene Product field the gene is shortly characterized. If there is no exact characterization
	possible, there are different types of classes available for a gene product. These can be		possible, there are different types of classes available for a gene product. These can be
	accessed in the drop down menu below the Gene Product entry and is entered in the entry after		accessed in the drop down menu below the Gene Product entry and is entered in the entry after
	choosing one. Examples are 'hypothetical protein' if no further information is available for		choosing one. Examples are 'hypothetical protein' if no further information is available for
	the gene product or 'conserved hypothetical protein' if there is at least one good hit to		the gene product or 'conserved hypothetical protein' if there is at least one good hit to
	a protein in another organism.		a protein in another organism.

Line 77:		Line 75:

	Below the description field there is the check box 'Experimental' which should be clicked if any		Below the description field there is the check box 'Experimental' which should be clicked if any
	of the results of the annotation are verified in the wet lab. Following are entries concerning		of the results of the annotation are verified in the wet lab. Following are entries concerning
	the COG (Cluster of orthologous group) functional classification, namely the COG number, COG		the COG (Cluster of orthologous group) functional classification, namely the COG number, COG
	funccat ID and COG funccat Description. These fields cannot be edited manually, but only		funccat ID and COG funccat Description. These fields cannot be edited manually, but only
	pressing the button 'Get' on the right. In the upcoming dialog a COG number can be selected and		pressing the button 'Get' on the right. In the upcoming dialog a COG number can be selected and
	the entries will be filled.		the entries will be filled.

	In the 'Function' field a short description of the function of the gene can be inserted.		In the 'Function' field a short description of the function of the gene can be inserted.
	A confidence for the complete annotation is also to be entered in the respective drop down field.		A confidence for the complete annotation is also to be entered in the respective drop down field.
	There are different confidence stati that can be chosen here. The strongest confidence is		There are different confidence stati that can be chosen here. The strongest confidence is
	'High confidence in function and specificity' and the weakest is 'Hypothetical protein'.		'High confidence in function and specificity' and the weakest is 'Hypothetical protein'.

	The following fields have already been described for the ~~[#RegionAnnotation~~ Region Annotation].		The following fields have already been described for the Region Annotation.

	[[File:annotationDialog.png]]		[[File:annotationDialog.png]]