Last updated September 9, 2009

GOAnnotations-PAMGO-Dickeya_dadantii_2009 README
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Contents

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1.  Introduction
2.  Gene Association File
3.  Columns in the Gene Association File
4.  Methods of Annotation
5.  Contact Information



1. Introduction
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GOAnnotations-PAMGO-Dickeya_dadantii_2009 Ð These annotations are the
result of a directed literature search aimed at annotating known and
putative virulence factors of Dickeya dadantii.  Annotations were done
by Dr. Brad Anderson in the laboratory of Dr. Nicole Perna at the
University of Wisconsin.  All annotations can be found at the ASAP
website, URL: https://asap.ahabs.wisc.edu/asap/home.php


2. Gene Association File
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The GOAnnotations-PAMGO-Dickeya_dadantii_2009 file uses the standard
file format for gene_association files of the Gene Ontology (GO)
Consortium. A more complete description of the file format is found at
http://www.geneontology.org/GO.format.annotation.shtml


3. Columns in the Gene Association File 
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 1: DB: database contributing the file 
 2: DB_Object_ID: Unique identifier for genes/gene products in an appropriate database.
 3: DB_Object_Symbol: a (unique and valid) symbol to which DB_Object_ID is matched. 
 4: Qualifier: (optional), flags that modify the interpretation of an annotation.
 5: GO ID: unique numeric identifier for the GO term.
 6: DB:Reference(|DB:Reference): the reference associated with the GO annotation. 
 7: Evidence code: the evidence code for the GO annotation.
 8: With (or) From: (optional), any With or From qualifier for the GO annotation. 
 9: Aspect: which ontology the GO term belongs (Function, Process or Component)
10: DB_Object_Name(|Name): (optional), a name of gene or gene product .
11: DB_Object_Synonym(|Synonym): (optional),  a gene symbol or other text.
12: DB_Object_Type: what kind of thing is being annotated.
13: taxon: taxonomic identifier of species encoding gene product.
14: Date: the date when GO annotation was made, in the format of YYYYMMDD.
15: Assigned_by: source of the annotation


4. Methods of Annotation
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All annotations were written based on a literature review of published
reports in Dickeya dadantii and closely related organisms.  The
majority of the annotations come from published work done on
D. dadantii.  Annotations that resulted from these works were given
appropriate experimental evidence codes.  Certain genes were
identified in D. dadantii that we strongly suspected to be involved in
virulence, but the supporting evidence did not come directly from
research in D. dadantii, but rather in a related organism.
Annotations written based on these reports were given Inferred by
Sequence Alignment based on our determination of orthology or strong
homology.  Orthology or homology was determined by analysis of
reciprocal blast hits combined with conservation of gene order between
organisms.  Initial predictions of orthology/homology were done on a
genome-wide basis, and each relationship pertaining to this set of
annotations was individually reviewed by an annotator.  The few
annotations carrying Inferred by Curator were given such evidence
because the references cited did not explicitly state or show data
confirming what was annotated, but could be reasonably deduced by one
familiar with the field, given in findings of the research.



5. Contact Information
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Questions about this file should be sent to: bdanderson@wisc.edu or ntperna@wisc.edu