September 2008 
 
File name:  gene_association.PAMGO_Atumefaciens.gz 
 
Synopsis: The compressed file, gene_association.PAMGO_Atumefaciens.gz,
contains the annotation of Agrobacterium tumefaciens C58 using Gene
Ontology (GO) terms.  Manual annotations were determined using
experimental data from literature references or reviewed computational
analyses by the annotator.  Information about the sequencing project
can be found at Agrobacterium.org.  Additional information can be
found at our database: http://agro.vbi.vt.edu/public/.  All annotation
of genes was carried out using guidelines established by the Gene
Ontology Consortium:

  http://geneontology.org/GO.annotation.conventions.shtml

The association file was formatted according to the guidelines
established in the GO Annotation File Format Guide:

  http://geneontology.org/GO.format.annotation.shtml

Annotation file format quality check was carried out using a script
provided by GO:

  http://www.geneontology.org/software/utilities/filter-gene-association.pl

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Description of Columns: 

1. DB: All sequences in this association file can be located in NCBI
with their corresponding accession numbers in the second column.

2. DB_Object_ID: Accession numbers retrieved from NCBI for
identification of individual gene products.

n3. DB_Object_Symbol: When available, the gene names were provided.
These common names are often found in literature.  When gene names
were not available, gene IDs, started with Atu, were provided.

4. Qualifier: (optional) Generally not used in this annotation file.

5. GO ID: GO terms were identified with this unique ID number.

6. DB:Reference(|DB:Reference): PubMed ID numbers were used for
experimental results.  When applicable, GO reference, GO_REF:0000027,
were used for sequence similarity searches via BLAST and labeled with
evidence code of ISS (applicable in column 7).
  
7. Evidence: All evidence codes in this column were assigned using the
guidelines provided in http://geneontology.org/GO.evidence.shtml

8. With (or) From: (optional) This optional field was used when the
evidence code in column 7 is ISS.

9. Aspect: The GO ID in column 5 would belong in one of these three
ontologies: function, process or component.

10. DB_Object_Name: (optional) When longer descriptions for gene
products were available, they were placed in this column.

11. DB_Object_Synonym (|Synonym): (optional) The gene IDs were used in
this column.  These gene IDs started with "Atu" can also be found in
the database located at the Virginia Bioinformatics Institute
(http://agro.vbi.vt.edu/public/).

12. DB_Object_Type: All annotated gene products were assigned as
"gene" in this column.

13. Taxon: NCBI taxon ID for Agrobacterium tumefaciens C58 is 176299,
which was used to identify the origin of all gene products annotated
in this file.

14. Date: The gene product was annotated on this date using the format
of YYYYMMDD.

15. Assigned_by: The annotation was carried out by PAMGO_GAT.
  
Additional references:

Goodner, B., G. Hinkle, et al. (2001). "Genome Sequence of the Plant
Pathogen and Biotechnology Agent Agrobacterium tumefaciens C58."
Science 294(5550): 2323-2328.

Wood, D. W., J. C. Setubal, et al. (2001). "The genome of the natural
genetic engineer Agrobacterium tumefaciens C58." Science 294:
2317-2323.

Source: Agrobacterium Genome Consortium (PAMGO project) 
 
Contact: setubal@vbi.vt.edu 
http://www.agrobacterium.org/ 
http://agro.vbi.vt.edu/public/
Funding by NSF/NRI-CSREES