GenDBWiki/TermsAndConcepts/AnnotationConcepts - Revision history

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2011-10-26T06:18:16Z

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imported>AlexanderGoesmann at 12:19, 1 December 2004

2004-12-01T12:19:48Z

← Older revision		Revision as of 14:19, 1 December 2004
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	== Status Region vs. Status Function ==		== Status Region vs. Status Function ==

	The '''region status''' can be used to indicate the progress of an ongoing annotation with respect to the reliability of each region. A specific '''region status''' could be set to indicate a potential frameshift or wrong gene start. Setting a special '''region status''' could also be used to distinguish the predictions from different gene finding tools, e.g. Glimmer and Critica.		The '''region status''' can be used to indicate the progress of an ongoing annotation with respect to the reliability of each region. A specific '''region status''' could be set to indicate a potential frameshift or wrong gene start. Setting a special '''region status''' could also be used to distinguish the predictions from different gene finding tools, e.g. Glimmer and Critica. The '''region status''' can be one of the following:

	* '''ignored''': Setting this status will ignore a region for all further analysis and also for all exports, e.g. to an EMBL file. Instead of deleting a region which is usually not supported by GenDB, the status should be set to ignored so that other annotators can still see that region and know immediately that someone already checked and discarded that region.		* '''ignored''': Setting this status will ignore a region for all further analysis and also for all exports, e.g. to an EMBL file. Instead of deleting a region which is usually not supported by GenDB, the status should be set to ignored so that other annotators can still see that region and know immediately that someone already checked and discarded that region.
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	* '''finished''': The region and function annotation of this region was assured by a human annotator. This region needs no more work and probably there is also some experimental evidence that confirms the annotation.		* '''finished''': The region and function annotation of this region was assured by a human annotator. This region needs no more work and probably there is also some experimental evidence that confirms the annotation.

	The '''functional status''' can be used to indicate the status of a region during an annotation. Whenever the function of a region is annotated a status from the following list should be assigned:		The '''functional status''' can be used to indicate the status of a region during an annotation with respect to the information content of a functional annotation. Whenever the function of a region is annotated a status from the following list should be assigned:

	* '''putative''': All regions are initially set to this status after creation. There is neither an automatic nor a manual function annotation.		* '''putative''': All regions are initially set to this status after creation. There is neither an automatic nor a manual function annotation.

imported>AlexanderGoesmann at 12:00, 1 December 2004

2004-12-01T12:00:37Z

← Older revision		Revision as of 14:00, 1 December 2004
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	== Status Region vs. Status Function ==		== Status Region vs. Status Function ==

	~~Set regional~~ status to ~~after checking~~ the ~~region, one~~ of the ~~following stati should~~ be ~~assigned~~ to ~~this~~ region~~: "~~		The '''region status''' can be used to indicate the progress of an ongoing annotation with respect to the reliability of each region. A specific '''region status''' could be set to indicate a potential frameshift or wrong gene start. Setting a special '''region status''' could also be used to distinguish the predictions from different gene finding tools, e.g. Glimmer and Critica.

	* ignored: ignore ~~this~~ region		* '''ignored''': Setting this status will ignore a region for all further analysis and also for all exports, e.g. to an EMBL file. Instead of deleting a region which is usually not supported by GenDB, the status should be set to ignored so that other annotators can still see that region and know immediately that someone already checked and discarded that region.
	* putative: ~~additional~~ status. ~~Do not use this one~~		* '''putative''': This status is assigned to regions that were just initially created, e.g. by a human annotator.
	* attention needed: the ~~status~~ of this region is ~~still~~ not ~~confident~~ and needs to be revised.		* '''attention needed''': This status indicates that the region annotation of this region is not reliable and needs to be revised.
	* status 1:		* '''status 1''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* status 2:		* '''status 2''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* status 3: ~~the function of these stati~~ can be defined ~~independently in~~ each project.		* '''status 3''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* finished: this region is assured and ~~does not need to be reprocessed~~.		* '''finished''': The region and function annotation of this region was assured by a human annotator. This region needs no more work and probably there is also some experimental evidence that confirms the annotation.

	~~Set~~ functional status to ~~after checking~~ the function~~, one~~ of the following ~~stati~~ should be assigned ~~to this region~~:		The '''functional status''' can be used to indicate the status of a region during an annotation. Whenever the function of a region is annotated a status from the following list should be assigned:

	* putative: ~~initial~~ status. There ~~has been~~ neither automatic nor manual ~~annota- tion~~.		* '''putative''': All regions are initially set to this status after creation. There is neither an automatic nor a manual function annotation.
	* attention needed: the functional ~~status~~ of this region is ~~still~~ not ~~confident~~ and needs to be revised.		* '''attention needed''': This status indicates that the functional annotation of this region is not reliable and needs to be revised.
	* automatically annotated: ~~This~~ function of this region ~~has been~~ automatically annotated, e.g. by Metanor. In the beginning of a manual annotation, most of the regions will have this function status.		* '''automatically annotated''': The function of this region was automatically annotated, e.g. by Metanor. In the beginning of a manual annotation, most of the regions will have this function status.
	* status 1: This status can be used to assign an individual property defined specifically for each project (sometimes unused).		* '''status 1''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* status 2: This status can be used to assign an individual property defined specifically for each project (sometimes unused).		* '''status 2''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* status 3: This status can be used to assign an individual property defined specifically for each project (sometimes unused).		* '''status 3''': This status can be used to assign an individual property defined specifically for each project (sometimes unused).
	* annotated: The function of this region has been verified by a human annotator. This implies that the annotation of such a region is done and therefore the region status will be usually set to ''finished''.		* '''annotated''': The function of this region has been verified by a human annotator. This implies that the annotation of such a region is done and therefore the region status will be usually set to ''finished''.

imported>AlexanderGoesmann at 10:44, 1 December 2004

2004-12-01T10:44:21Z

@@ Line 1: / Line 1: @@
 __NOTOC__
-= Details about the GenDB Annotation Concept =
+= Details about specific GenDB Concepts =
-* Annotation Region vs. Annotation Function
+The following sections illustrate some specific concepts that are implemented within the GenDB genome annotation system. Before you start annotating a genome you should read these sections in order to understand how the system works with your data and how some information is stored systematically to facilitate further analyses.
-* never delete
-* status function vs. status region
+== Annotation Concepts ==
-* latest annotation function and region

imported>AlexanderGoesmann at 09:48, 14 October 2004

2004-10-14T09:48:18Z

← Older revision	Revision as of 11:48, 14 October 2004
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Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= Details about the GenDB Annotation Concept =

* Annotation Region vs. Annotation Function
* never delete
* status function vs. status region
* latest annotation function and region