UniProtKB-GOA README FOR GP_ASSOCIATION.GOA_UNIPROT --------------------------------------------------- 1. Contents ------------ 1. Contents 2. Introduction 2. Introduction ---------------- UniProtKB-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 the knowledge of the gene product roles in cells is still accumulating and changing. In the UniProtKB-GOA project, this vocabulary is applied to all proteins described in the UniProt (Swiss-Prot and TrEMBL) Knowledgebase. For full information on the UniProtKB-GOA project, please go to: http://www.ebi.ac.uk/GOA This readme describes the format of the gp_association.goa_uniprot file. This file is a product of the gene_association.goa_uniprot file, that is designed to provide the minimal information required to describe a GO annotation. This format of this file is described below, however as the format is currently being discussed by the GO Consortium it is therefore subject to change. For further information, please see: http://wiki.geneontology.org/index.php/Annotation_File_Format_Proposal#Proposed_file_format This file currently consists of 11 tab-separated fields; their contents are described below. 1. DB Database from which annotated entry has been taken. This file will contain one of either: UniProtKB or IPI This field equates to column 1 in the GAF2.0 format. 2. DB_Object_ID A unique identifier in the database for the item being annotated. Here: an accession number or identifier of the annotated protein - a UniProtKB accession number or IPI identifier Example: O00165 This field equates to column 2 in the GAF2.0 format. 3. Qualifier This column is used for flags that modify the interpretation of an annotation. If not null, then values in this field can equal: NOT, colocalizes_with, contributes_to, NOT | contributes_to, NOT | colocalizes_with Example: NOT This field equates to column 4 of the GAF2.0 format 4. GO ID The GO identifier for the term attributed to the DB_Object_ID. Example: GO:0005634 This field equates to column 5 of the GAF2.0 format 5. DB:Reference A single reference cited to support an annotation. Where an annotation cannot reference a paper, this field will contain a GO_REF identifier. See: http://www.geneontology.org/doc/GO.references for an explanation of the reference types used. Examples: PMID:9058808 DOI:10.1046/j.1469-8137.2001.00150.x GO_REF:0000002 GO_REF:0000020 GO_REF:0000004 GO_REF:0000003 GO_REF:0000019 GO_REF:0000023 GO_REF:0000024 This field equates to column 6 in the GAF2.0 format. 6. Evidence code One of either EXP, IMP, IC, IGI, IPI, ISS, IDA, IEP, IEA, TAS, NAS, NR, ND or RCA. Example: TAS This field equates to column 7 in the GAF2.0 format. 7. With An additional identifier to support annotations using certain evidence codes (including IEA, IPI, IGI, IC and ISS evidences). Examples: UniProtKB:O00341 InterPro:IPROO1878 Ensembl:ENSG00000136141 GO:0000001 EC:3.1.22.1 This field equates to column 8 in the GAF2.0 format 8. Extra taxon ID This taxon id should inform on the other organism involved in an multi-species interaction. An extra taxon id can only be used in conjunction with terms that have the biological process term 'GO:0051704; multi-organism process' or the cellular component term 'GO:0043657; host cell' as an ancestor. This taxon id should inform on the other organism involved in the interaction. For further information please see: http://www.geneontology.org/GO.annotation.conventions.shtml#interactions This field has been separated from the dual taxon id format allowed in the taxon (column 13 in GAF2.0 format). 9. Date The date of last annotation update in the format 'YYYYMMDD' Example: 20050101 This field equates to column 14 in the GAF2.0 format. 10. Assigned_by Attribute describing the source of the annotation. One of either UniProtKB, AgBase, BHF-UCL, CGD, DictyBase, EcoCyc, EcoWiki, Ensembl, FB, GDB, GeneDB, GR (Gramene), HGNC, Human Protein Atlas, LIFEdb, MGI, PAMGO_GAT, Reactome, RGD, Roslin Institute, SGD, TAIR, TIGR, ZFIN, IntAct, PINC (Proteome Inc.) or WormBase. Example: UniProtKB This field equates to column 15 in the GAF2.0 format. 11. Annotation Extension (N.B. Until annotation practices are finalised, this column will remain empty) Contains cross references to other ontologies/databases that can be used to qualify or enhance the annotation. The cross-reference is prefaced by an appropriate GO relationship; references to multiple ontologies can be entered. Example: part_of(CL:0000084) occurs_in(GO:0009536) has_input(CHEBI:15422) has_output(CHEBI:16761) has_participant(UniProtKB:Q08722) part_of(CL:0000017)|part_of(MA:0000415) This field equates to column 16 in the GAF2.0 format. 12. Gene_Product_Form_ID The fully-qualified unique identifier of a specific spliceform of the protein described in column 2 (DB_Object_ID) Example:UniProtKB:O43526-1 This field equates to column 17 in the GAF2.0 format.