GenDBWiki/WebDocumentation/DialogWindows/Supporting Observations Update - Revision history

Admin: 14 revisions

2011-10-26T06:15:40Z

14 revisions

← Older revision	Revision as of 08:15, 26 October 2011
(No difference)

imported>SebastianKonietzny at 12:00, 25 April 2006

2006-04-25T12:00:57Z

← Older revision		Revision as of 14:00, 25 April 2006
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	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$~~supportupdatescol2~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$sou_leiste2_smaller.png]]

	'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.		'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.

imported>SebastianKonietzny at 11:54, 25 April 2006

2006-04-25T11:54:56Z

← Older revision		Revision as of 13:54, 25 April 2006
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	----		----
	Following is an overview of the most important elements (column names) of the single entries in the result-list:		'''Following is an overview of the most important elements (column names) of the single entries in the result-list:'''

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]

imported>SebastianKonietzny at 11:54, 25 April 2006

2006-04-25T11:54:14Z

← Older revision		Revision as of 13:54, 25 April 2006
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	=== Interpreting the results ===		=== Interpreting the results ===

	'''Example for a result list:		'''Example for a result list:'''

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$attachment_sou_list.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$attachment_sou_list.png]]

imported>SebastianKonietzny at 11:29, 25 April 2006

2006-04-25T11:29:42Z

← Older revision		Revision as of 13:29, 25 April 2006
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	=== Interpreting the results ===		=== Interpreting the results ===

	'''Example for a result list:~~''' '''''Note that this is an old picture which shows non-actual column-names!'''''~~		'''Example for a result list:
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$~~supportobslist2~~.png]]
			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$attachment_sou_list.png]]

	----		----

imported>SebastianKonietzny at 11:23, 25 April 2006

2006-04-25T11:23:43Z

imported>SebastianKonietzny at 18:45, 12 April 2006

2006-04-12T18:45:52Z

← Older revision		Revision as of 20:45, 12 April 2006
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	'''This method serves two aspects in managing the supporting observations of the CDS-regions of a contig:'''		'''This method serves two aspects in managing the supporting observations of the CDS-regions of a contig:'''

	It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the ''supporting observations'' that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation ~~and~~ the ~~most significant~~ supporting observation ~~(of the specified~~ tool) if it exists. A html-link allows you to get quickly into the annotation dialog of that gene.		It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the ''supporting observations'' that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation (including the best currently used supporting observation for that tool-if it exists) and finally the up-to-date most promising candidate observation to improve evidence of the annotation . A html-link allows you to get quickly into the annotation dialog of that gene.

	Additionally it's possible to enrich the result-list by observations that are proposed as the currently best candidates to be used in the annotations when there haven't been used any supporting observations yet!		Additionally it's possible to enrich the result-list by observations that are proposed as the currently best candidates to be used in the annotations when there haven't been used any supporting observations yet!

imported>SebastianKonietzny at 18:38, 12 April 2006

2006-04-12T18:38:11Z

← Older revision		Revision as of 20:38, 12 April 2006
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	----		----

	This method ~~performs~~ two aspects ~~for~~ managing the supporting observations of the CDS-regions of a contig:		'''This method serves two aspects in managing the supporting observations of the CDS-regions of a contig:'''

	It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the ''supporting observations'' that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation and the most significant supporting observation (of the specified tool) if it exists. A html-link allows you to get quickly into the annotation dialog of that gene.		It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the ''supporting observations'' that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation and the most significant supporting observation (of the specified tool) if it exists. A html-link allows you to get quickly into the annotation dialog of that gene.

imported>SebastianKonietzny at 18:36, 12 April 2006

2006-04-12T18:36:49Z

← Older revision		Revision as of 20:36, 12 April 2006
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	=== Introduction ===		=== Introduction ===
	----		----
	'''Supporting Observations''': Functional Annotations of a region object (e.g. a CDS region) ~~significantly~~ rely on information that is provided by precomputed functional observations of various tools suitable to detect functional characteristics. For example Blast tools may detect homology information for a regions's sequence that allows to ~~infere~~ some functional meaning of the region object (e.g. what kind of gene it is!). It's useful to list those related observations in the framework of the functional annotation. Observations listed as attributes of the annotation object are referred to as ''supporting observations''. They serve to provide evidence to the content of the annotation.		'''Supporting Observations''': Functional Annotations of a region object (e.g. a CDS region) considerably rely on information that is provided by precomputed functional observations of various tools suitable to detect functional characteristics. For example Blast tools may detect homology information for a regions's sequence that allows you to infer some functional meaning of the region object (e.g. what kind of gene it is!). It's useful to list those related observations in the framework of the functional annotation. Observations listed as attributes of the annotation object are referred to as ''supporting observations''. They serve to provide evidence to the content of the annotation.
	----		----

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	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatesintro.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatesintro.png]]

			'''The CDS-regions will be taken from the contig, that is currently selected in the session!'''

	'''Select from Blast-tools:'''		'''Select from Blast-tools:'''
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	=== Interpreting the results ===		=== Interpreting the results ===

	'''Example for a result list:'''		'''Example for a result list:''' '''''Note that this is an old picture which shows non-actual column-names!'''''
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportobslist2.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportobslist2.png]]

	----		----
			Following is an overview of the most important elements (column names) of the single entries in the result-list:

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol2.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol2.png]]
	~~[[Image~~:~~GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatesintro~~.~~png]]~~
			'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.
			'''CURRENT_BEST_EVALUE''': Evalue of the best (currently used) supporting observation (corresponding to the specified tool).
			'''CURRENT_BEST_SCORE''': Score of the best (currently used) supporting observation (corresponding to the specified tool).
			'''CURRENT_BEST_DESCR''': Description of the best (currently used) supporting observation (corresponding to the specified tool).
			'''CURRENT_BEST_DATE''': Date of the best (currently used) supporting observation (corresponding to the specified tool).
			'''CURRENT_AnnF_DESC''': Description of the current annotation function.
			'''CURRENT_AnnF_DATE''': Date of creation of the current annotation function.
			'''PROPOSED_EVALUE''': Evalue of the proposed observation.
			'''PROPOSED_SCORE''': Score of the proposed observation.
			'''PROPOSED_DESCR''': Description of the proposed observation.
			'''PROPOSED_DATE''': Date of creation of the proposed observation.
			'''ACTIONS''': Opens the annotation dialog.
			'''ANNOTATOR''': Name of the annotator that created the current annotation function.

imported>SebastianKonietzny at 18:09, 12 April 2006

2006-04-12T18:09:34Z

@@ Line 1: / Line 1: @@
 __NOTOC__
-This method checks for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the observation objects that are currently referred to from the functional annotations. Observations objects that are referred from a functional annotation are called ''supporting observations''. They serve to provide evidence to the content of the annotation.
+'''This method considers for a subset of the CDS-regions (of a contig) whether significant functional observations of a specified tool exist that are not yet used in the functional annotation of the CDS-regions.'''
-Check for better candidates than the observations that are currently used in functional annotation (called 'supporting observations'!)
+=== Introduction ===
 [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol1smaller.png]]
 [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatescol2.png]]
 [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$Supporting_Observations_Update$supportupdatesintro.png]]

← Older revision		Revision as of 13:23, 25 April 2006
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	'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.		'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.

	'''CURRENT_BEST_EVALUE''': Evalue of the best (currently used) supporting observation (corresponding to the specified tool).		'''CURRENT_BEST_EVALUE''': Evalue of the best (currently used) supporting observation (corresponding to the specified tool).

	'''CURRENT_BEST_SCORE''': Score of the best (currently used) supporting observation (corresponding to the specified tool).		'''CURRENT_BEST_SCORE''': Score of the best (currently used) supporting observation (corresponding to the specified tool).

	'''CURRENT_BEST_DESCR''': Description of the best (currently used) supporting observation (corresponding to the specified tool).		'''CURRENT_BEST_DESCR''': Description of the best (currently used) supporting observation (corresponding to the specified tool).

	'''CURRENT_BEST_DATE''': Date of the best (currently used) supporting observation (corresponding to the specified tool).		'''CURRENT_BEST_DATE''': Date of the best (currently used) supporting observation (corresponding to the specified tool).

	'''CURRENT_AnnF_DESC''': Description of the current annotation function.		'''CURRENT_AnnF_DESC''': Description of the current annotation function.

	'''CURRENT_AnnF_DATE''': Date of creation of the current annotation function.		'''CURRENT_AnnF_DATE''': Date of creation of the current annotation function.

	'''PROPOSED_EVALUE''': Evalue of the proposed observation.		'''PROPOSED_EVALUE''': Evalue of the proposed observation.

	'''PROPOSED_SCORE''': Score of the proposed observation.		'''PROPOSED_SCORE''': Score of the proposed observation.

	'''PROPOSED_DESCR''': Description of the proposed observation.		'''PROPOSED_DESCR''': Description of the proposed observation.

	'''PROPOSED_DATE''': Date of creation of the proposed observation.		'''PROPOSED_DATE''': Date of creation of the proposed observation.

	'''ACTIONS''': Opens the annotation dialog.		'''ACTIONS''': Opens the annotation dialog.

	'''ANNOTATOR''': Name of the annotator that created the current annotation function.		'''ANNOTATOR''': Name of the annotator that created the current annotation function.