Annotation of close strain sets - Revision history

FolkerMeyer at 20:03, 4 December 2006

2006-12-04T20:03:43Z

RossOverbeek: /* Step 6: Continuous Refinement Via Analysis of Literature */

2006-08-26T21:53:00Z

Step 6: Continuous Refinement Via Analysis of Literature

RossOverbeek: /* Step 5: Improvement of Annotation Via New Subsystems */

2006-08-26T21:52:50Z

Step 5: Improvement of Annotation Via New Subsystems

RossOverbeek: /* Step 4: Resolution of Conflicts */

2006-08-26T21:52:33Z

Step 4: Resolution of Conflicts

RossOverbeek: /* Step 3: Annotation of Prophages and Mobil Elements */

2006-08-26T21:52:03Z

Step 3: Annotation of Prophages and Mobil Elements

RossOverbeek at 15:46, 23 August 2006

2006-08-23T15:46:57Z

FolkerMeyer at 16:08, 16 August 2006

2006-08-16T16:08:12Z

FolkerMeyer: Annotation of close strains moved to Annotation of close strain sets

2006-08-13T23:12:22Z

Annotation of close strains moved to Annotation of close strain sets

VeronikaVonstein: Annotation moved to Annotation of close strains

2006-08-13T23:08:42Z

Annotation moved to Annotation of close strains

FolkerMeyer at 16:30, 13 August 2006

2006-08-13T16:30:58Z

@@ Line 1: / Line 1: @@
 == Annotation of Genomes: ==
-=== Standard Operating Procedure ===
+=== Standard Operating Procedure (FIG|SOP002)===
 === Introduction ===

@@ Line 97: / Line 97: @@
 Normal subsystem maintenance occurs constantly.  The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems.  These activities produce a gradual improvement in the quality of annotations for all genomes.  All new annotations are logged as they are made.
-==== Step 6: Continuous Refinement Via Analysis of Literature ====
+==== Step 5: Continuous Refinement Via Analysis of Literature ====
 Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results.  Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class).  More often, these new results are used as the basis for new subsystems and have a broader impact.

@@ Line 93: / Line 93: @@
   potential_conflicts GenomeToBeAnnotated  FileOfGenomesGivingContext
-==== Step 5: Improvement of Annotation Via New Subsystems ====
+==== Step 4: Improvement of Annotation Via New Subsystems ====
 Normal subsystem maintenance occurs constantly.  The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems.  These activities produce a gradual improvement in the quality of annotations for all genomes.  All new annotations are logged as they are made.

@@ Line 87: / Line 87: @@
-==== Step 4: Resolution of Conflicts ====
+==== Step 3: Resolution of Conflicts ====
 FIGfams are not always annotated consistently.  This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family.  In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions.  The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function.  Execution of the following command will produce a list of conflicts that should be examined by an annotator:
   potential_conflicts GenomeToBeAnnotated  FileOfGenomesGivingContext
 ==== Step 5: Improvement of Annotation Via New Subsystems ====

← Older revision		Revision as of 21:52, 26 August 2006
Line 85:		Line 85:
	The tentative metabolic reconstruction is formed (including subsystems from both lists).		The tentative metabolic reconstruction is formed (including subsystems from both lists).

−	~~==== Step 3: Annotation of Prophages and Mobil Elements ====~~

−	~~For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of~~
−
−	~~mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext~~
−	~~mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext~~
−
−	~~will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged.~~

	==== Step 4: Resolution of Conflicts ====		==== Step 4: Resolution of Conflicts ====

@@ Line 68: / Line 68: @@
 Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam).  The process begins with
-  potentially_missed_assignments GenomeToBeAnnotated  FileOfGenomesGivingContext
+  potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext
-This command will produce a list of assignments that may have been missed.  This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located.  The tool produces a list of possibly missed assignments that must be checked by an annotator.
+This command will produce a list of assignments that may have been missed.  This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located.  The tool produces a list of possibly missed assignments that must be checked by an annotator.  The assignments are installed as
 Once the list of possibly missed assignments has been processed, the following command can be run:
-  add_to_subsystems User GenomeToBeAnnotated  FileOfGenomesGivingContext
+  add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext
 This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome.  This set of subsystems will then be split into two lists:

@@ Line 24: / Line 24: @@
 '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG).  These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP).  The important properties of these families are as follows:
-#	Two PEGs which both occur within a single FIGfam are believed to have the same function.
+# Two PEGs which both occur within a single FIGfam are believed to have the same function.
 # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family.
 '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems.

← Older revision	Revision as of 23:12, 13 August 2006
(No difference)

← Older revision	Revision as of 23:08, 13 August 2006
(No difference)

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 Genes other than PEGs can also be assigned functions (e.g., SSU rRNA).  However, in most cases the functions assigned to genes other than PEGs tend not to be problematic.  This document will focus solely on annotation of PEGs.
-Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation.  In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism.  We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes.  Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes.  This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes.
+'''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation.  In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism.  We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes.  Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes.  This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes.
 We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms).  This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere.