!version: $Revision: 2.2 $
!date: $Date: 2002/04/26 23:00:03 $
!Title: Rice to Go association 
!Gramene: A Comparative mapping Resource
!www.garmene.org
!Rice Protein database
!http://www.gramene.org/perl/protein_search
!Rice to Go association Release 1.0 
!
Read me file for rice protein associations to GO.

CONTENTS

1. Rice Protein Database at Gramene

2. Statistics

3. Methodology

3. File Format

5. Contacts

6. Acknowledgements

***********************************************************



1.  Rice Protein Database Release 4.1.0, Feb. 25, 2002  http://www.gramene.org
    
    Rice to Go association Release 1.0 (present Association file rice2GO.txt)

Gene Ontology associations provided for rice belongs to following
taxons. The information on Gene products is available at

http://www.gramene.org/perl/protein_search


Taxon                                                         NCBI Tax.ID    Assignments

Oryza                                                      	  4527		

Oryza sativa (rice)*                                           	  4530*		 5877
   Oryza sativa (subspecies indica ) (Indian rice)        	 39946		 1177
   Oryza sativa (subspecies japonica) (Japanese rice)   	 39947		13890

Oryza alta                                                   	 52545		    9
Oryza australiensis                                            	  4532		    8
Oryza barthii                                           	 65489		    5
Oryza brachyantha                                              	  4533		    4
Oryza eichingeri                                             	 29689		   11
Oryza glaberrima (African rice)                          	  4538		    7
Oryza glumaepatula                                             	 40148		    4
Oryza grandiglumis                                        	 29690		   12
Oryza granulata                                         	110450		    4
Oryza latifolia                                               	  4534		   11
Oryza longiglumis                                       	 83309		    6
Oryza longistaminata (long-staminate rice)                     	  4528		   34
Oryza malampuzhaensis                                   	127571		    -
Oryza meridionalis                                         	 40149		    5
Oryza meyeriana                                           	 83307		   11
Oryza minuta                                                  	 63629		   11
Oryza nivara                                                 	  4536		    5
Oryza officinalis                                         	  4535		   26
Oryza perennis                                            	 29691		    -
Oryza punctata                                                    4537		    6
Oryza rhizomatis                                           	 65491		    9
Oryza ridleyi                                                  	 83308		    6
Oryza rufipogon (common wild rice)                            	  4529		   26
Oryza schlechteri                                       	110451		    6
Oryza sp. (rice)                                        	 52841		    -

                                                                              ___________
                                                                  
                                                                  (TOTAL)       21170 


* Oryza sativa (Tax. ID 4530), was scored in the association files only when there was no 
  information available for subspecies, indica (Tax. ID 39946) or japonica (Tax. ID 39947). 
  In such case only information available on organism was for the O. sativa (Tax. ID 4530).

2. STATISTICS:


1). No. of entries in Rice protein database at Gramene: 8281
    No. of rice entries in SWISSPROT: 393
    No. of rice entries in TrEMBL   : 7888

2). Total number of GO associations mapped**: 9866 (http://www.gramene.org/perl/ontology/search_term?id=GO:0003673)
   
    GO:Function: 5599
    GO:Process: 2881 
    GO:Component: 1386

** It represents total no. of times the Gene Ontology terms have been associated with rice proteins listed in the file. 
   Caution: It does not represent the total number of terms associated with the proteins.

3. Methodology

The mappings were done using the protein entries for rice from following databases and the GO association files.

Databases used:

	SWALL release Jan' 2002
	Swissprot release 40.1
	TrEMBL release 19.9

Files used for mapping the GO terms to Gene products:

	protein2ipr.dat      interpro2go   (both vailable from ftp://ftp.ebi.ac.uk/pub/databases/interpro/)
 
	spkw2go              ec2go         (available from http://www.geneontology.org/)


4. File Format

The file format is based on the guidelines provided by the Gene Ontology
Consortium (http://www.geneontology.org/doc/GO.annotation.html#file).  

	1.  DB
	    Database: Gramene
    	    Example: GR
    
	2.  DB_Object_ID
	    ID: Accession number    
            Example: Q9M6X2
    
	3.  DB_Object_Symbol
            symbol: Gene product symbol (if not available then ID from 2. is used)
            Example: ADH2
            Example: Q9AXD9 (when gene product symbol not available)
    
	4.  NOT
            Blank in present file
    
	5.  GOid
            The GO identifier for the term attributed to the DB_Object_ID.
            Example: GO:0004024
    
	6.  DB:Reference
            Examples: InterPro:IPR002048 
            Examples: GR:5367|PMID:7914763
    
	7.  Evidence
            Evidence codes
            Example: IEA
            Example: IDA
	    
	8.  With
            Blank in present file
    
	9.  Aspect
            Representing one of the three ontologies viz., P (biological process), F (molecular function) or C (cellular component).
            Example: F
    
	10. DB_Object_Name
            Name of the gene product
            Example: 3-hydroxy-3-methylglutaryl-CoA reductase

	11. Synonym
            Blank in present file
    
	12. DB_Object_Type
            Type of entity is being annotated (transcript or protein)
            Example: protein
    
	13. Taxon_ID
            NCBI Taxonomic ID
            Example: taxon:4530 (Oryza sativa)


5. Contacts
 
For queries please send an e. mail to gramene@gramene.org


6. Acknowledgements

We acknowledge Daniel Barrell and Nickola Mulder from EBI, UK,  for their help on mapping the GO associations.