PDB GOA README -------------- 1. Contents ------------ 1. Contents 2. Introduction 3. File format 4. Addition of GO assignments from other data sources 5. Contacts 6. Copyright Notice 2. Introduction ---------------- GOA (GO Annotation@EBI) is a project run by the European Bioinformatics Institute that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The goal of the Gene Ontology Consortium is to produce a dynamic controlled vocabulary that can be applied to all eukaryotes, even while knowledge of gene and protein roles in cells is still accumulating and changing. In the GOA project, this vocabulary will be applied to a non-redundant set of proteins described in the SWISS-PROT, TrEMBL and Ensembl databases that collectively provide complete proteomes for Homo sapiens and other organisms. This file describes GO annotations to PDB entries inferred by the manual and electronic annotation of GO terms to Swiss-Prot and TrEMBL entries. For futher information please refer to our web site at: http://www.ebi.ac.uk/GOA 3. File format --------------- gene_association.goa_pdb This file contains GO assignments to PDB entries We have complied with the file format described by the GeneOntology consortium for annotation files (http://www.geneontology.org/GO.annotation.html#file) 1. DB Database from which entry has been taken. ie: 'PDB' 2. DB_Object_ID A unique identifier in the DB for the item being annotated. Here: ID of the PDB entry. Example: '1BDL' 3. DB_Object_Symbol Chain ID of the PDB entry Example: 'A' 4. NOT Always empty. 5. GOid The GO identifier for the term attributed to the DB_Object_ID. Example: 'GO:0005625' 6. DB:Reference Explains the method used to infer the annotation. Examples: GOA:manual, GOA:interpro, GOA:spkw, GOA:spec. 7. Evidence Always 'IEA'. 8. With Swiss-Prot/TrEMBL AC from where the annotation is inferred from. Example: 'SPTR:O00341' 9. Aspect One of the three ontologies: P (biological process), F (molecular function) or C (cellular component). Example: 'P' 10. DB_Object_Name Always empty 11. Synonym Always empty. 12. DB_Object_Type What kind of entity is being annotated. Always 'protein_structue' 13. Taxon_ID Identifier for the species being annotated. Example: 'taxon:9606' 14. Date The date of last annotation update in the format 'YYYYMMDD' eg: 20030228 15. Assigned_By Attribute describing the source of the annotation. Always 'SPTR' 4. Assignment of GO terms to SWISS-PROT/TrEMBL/Ensembl data ------------------------------------------------------------ In this release, we use four data sources to assign GO terms to proteins. A) GOA:manual Curators have read the abstract or full paper and assigned the GO terms manually to a Swiss-Prot/TrEMBL entry. Here we have used a Swiss-Prot->PDB mapping to infer these annotations. B) GOA:interpro Transitive assignment using InterPro matches on Swiss-Prot/TrEMBL entries. Further mapped to PDB entries. C) GOA:spkw Transitive assignment using SWISS-PROT keywords. Further mapped to PDB entries. D) GOA:spec Transitive assignment using enzyme codes. Further mapped to PDB entries. The files interpro2go, spkw2go and ec2go are found at http://www.geneontology.org/index.html#classification. 5. Contacts ----------- Please direct any questions to goa@ebi.ac.uk We welcome any feedback. 6. Copyright Notice -------------------- GOA - GO Annotation@EBI Copyright 2003 (C) The European Bioinformatics Institute. This README and the accompanying databases may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy. $Date: 2003/05/02 10:57:16 $