!version: $Revision: 1.18 $ !date: $Date: 2009/09/23 20:59:28 $ !Title: Rice to Go association !Gramene: A Comparative mapping Resource !www.garmene.org !Rice Protein database !http://www.gramene.org/perl/protein_search !Read me file for rice protein associations to GO. CONTENTS 1. Rice Protein Database at Gramene 2. Statistics 3. Methodology 4. File Format 5. Contacts 6. Acknowledgements *********************************************************** 1. Rice Protein Database Release 30, September 23, 2009 http://www.gramene.org 2. STATISTICS: Gramene Oryza Protein GO annotation Statistics Sep.23, 2009 Total number of Oryza proteins 144261 # proteins from SWISS-PROT 995 # proteins from TrEMBL 143266 Total number of Gene ontology association 119180 # GO Biological Process associations 15170 # GO Cellular Component associations 76934 # GO Molecular Function associations 24903 Total number associations with only IEA evidence code 68029 Total number associations with only non-IEA evidence code 45020 Total number associations with IEA and non-IEA evidence code 6131 Total number of gene products with at least one GO annotation 72671 # of gene products annotated with at least one biological process term 11495 # of gene products annotated with at least one cellular component term 67296 # of gene products annotated with at least one molecular functionterm 13618 # of gene products annotated to GO:0000004 unknown_process 0 # of gene products annotated to GO:0005554 unknown_function 1 # of gene products annotated to GO:0008372 unknown_component 0 evidence code # gene product IAGP 1 IC 1189 IDA 52 IEA 42866 IEP 104 IGI 21 IMP 78 IPI 5 ISS 195 NOT 40 RCA 40421 SM 3 TAS 25 # of genes/products that have at least one GO annotation in all of the three ontologies (fully annotated) 6935 Species NCBI Tax. ID # of gene products annotated Oryza sativa (japonica cultivar-group) 39947 57979 Oryza sativa (indica cultivar-group) 39946 27238 Oryza sativa 4530 5145 Oryza rufipogon 4529 282 Oryza nivara 4536 159 Oryza officinalis 4535 42 Oryza brachyantha 4533 41 Oryza barthii 65489 36 Oryza glaberrima 4538 35 Oryza longistaminata 4528 30 Oryza meridionalis 40149 29 Oryza australiensis 4532 28 Oryza granulata 110450 27 Oryza punctata 4537 27 Oryza glumipatula 40148 25 Oryza alta 52545 24 Oryza coarctata 77588 21 Oryza minuta 63629 16 Oryza rhizomatis 65491 14 Oryza eichingeri 29689 14 Oryza meyeriana 83307 12 Oryza latifolia 4534 12 Oryza grandiglumis 29690 10 Oryza ridley 83308 9 Oryza sativa 4530 8 Oryza australiensis 4532 8 Oryza punctata 4537 8 Oryza officinalis 4535 7 Oryza latifolia 4534 6 Oryza barthii 65489 6 Oryza rhizomatis 65491 5 Oryza longiglumis 83309 5 Oryza schlechteri 110451 5 Oryza sativa f. spontanea IRRI 81916 364099 4 Oryza nivara 4536 4 Oryza glumipatula 40148 4 Oryza grandiglumis 29690 4 Oryza granulata 110450 3 Oryza sativa f. spontanea IRRI 105360 364100 3 Oryza meridionalis 40149 3 Oryza eichingeri 29689 2 Oryza alta 52545 2 Oryza sp. Poi-6 389215 1 Oryza malampuzhaensi 127571 1 Oryza sativa subsp. japonica 39947 1 3. Methodology Databases used: Swiss-Prot and TrEMBL Gene ontology associations based on Gramene curation and Interpro assignments. 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) 14. Date Date when the mappings were done (in this case is the date of release for protein database) Example: 20020225 15. Assigned_by The database which made the annotation Example: GR 5. Contacts For queries please send an e. mail to gramene@gramene.org 6. Acknowledgements We acknowledge Daniel Barrell and Nicola Mulder from EBI, UK, for their help on mapping the GO associations.