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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
-----------------------
gene_association.PAMGO_Mgrisea.gz -- A source for Magnaporthe grisea
GO annotations. These annotations are based on both experimental data
from scientific literature and orthologs identified by stringent
computational approaches. Annotations were done by the Magnaporthe
grisea genome annotation team at North Carolina State University. The
annotating database is identified in column 15.

2. Gene Association File
----------------------------
The gene_association.PAMGO_Mgrisea.gz 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 
--------------------------------------------
 1: DB: database contributing the file, including NCBI and UniProtKB.
 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. A DB_Object_ID is filled in this column when a symbol
    is not available.
 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. GO_REF:0000028 records the annotation method used by
    the Magnaporthe grisea genome annotation team.
 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 (PAMGO_MGG)

4. Methods of Annotation
-----------------------------
Two types of methods were used in annotating the proteins. One is
literature-based GO annotation, and the other is ortholog-based GO
annotation. For the literature-based GO annotation, an annotator read
research articles, identified gene products, then assigned appropriate
GO terms and evidence code to these gene products. More than 2,730
proteins of Magnaporthe grisea were annotated based on experimental
data from scientific literature. Ortholog-based GO annotation used
stringent computational approaches as follows: Standard BLASTP from
NCBI was used to iteratively search reciprocal best hits and thus
identified orthologs between predicted proteins of Magnaporthe grisea
and GO proteins from multiple organisms with published association to
GO terms. The alignments were manually reviewed for those hits with
e-value equal to zero and with 80% or better coverage of both query
and subject sequences, and for those hits with e-value equal to 1e-20
or better, pid equal to 35 or better, and sequence coverage equal to
80% or better. From the manually reviewed computational analysis, we
assigned functions to 2,870 hypothetical proteins. Eighty percent of
functional assignments were based on reciprocal best blast hits with
an e-value equal to zero.

5. Contact Information
---------------------------
Questions about this file should be sent to: smeng@ncsu.edu