This page describes the Gene Product Information (GPI) 2.0 format. This format has not yet been implemented in GO but is provided to help with the changeover from previous GPAD/GPI versions.

Currently under construction

Gene Product Information (GPI) files

This guide lays out the format specifications for the Gene Product Information (GPI) 2.0 format. Note that the GPI file is the companion file for the GPAD file. Both files should be submitted together using the same version.

The Gene Ontology Consortium stores annotation data, the representation of gene product attributes using GO terms, in tab-delimited text files. Each line in the file represents a single association between a gene product and a GO term with a certain evidence code and the reference to support the link.

GO also provides annotations as GAF files. For more general information on annotation, please see the Introduction to GO annotation.

Changes from the GPI 1.2 to GPI 2.0

Header

  • The gpi-version header must read 2.0 for this format.

Columns

  • Columns 1 & 2 from the GPI 1.2 are now combined in a single column containing an id in CURIE syntax, e.g. UniProtKB:P56704.**
  • NCBI taxon ids are to be prefixed with ‘NCBITaxon:’ to indicate the source of the id, e.g. NCBITaxon:6239
  • Dates must now follow the ISO-8601 format, e.g. YYYY-MM-DD; time may be included as YYYY-MM-DDTHH:MM:SS

    Gene Product Information (GPI) 2.0 format

GPI Header

All annotation files must start with a single line denoting the file format. For GPI it is as follows:

!gpi-version: 2.0

Other information, such as contact details for the submitter or database group, useful links, etc., can be included in an association file by prefixing the line with an exclamation mark (!); such lines will be ignored by parsers.

Required information to provide in the header:

!generated-by: database listed in dbxrefs.yaml
!date-generated: YYYY-MM-DD or YYYY-MM-DDTHH:MM

GPI fields

The file format comprises 10 tab-delimited fields. Fields with multiple values (for example, gene product synonyms) should separate values by pipes.

Column Content Required? Cardinality Example  
1 DB:DB_Object_ID required 1 UniProtKB:Q4VCS5  
2 DB_Object_Symbol required 1 AMOT  
3 DB_Object_Name optional 0 or greater Angiomotin  
4 DB_Object_Synonym(s) optional 0 or greater E230009N18Rik KIAA1071
5 DB_Object_Type required 1 PR:000000001  
6 DB_Object_Taxon required 1 taxon:9606  
7 Encoded_by optional 0 or greater EXAMPLE NEEDED  
8 Parent_Protein optional 0 or 1 UniProtKB:Q4VCS5  
9 Protein_Containing_Complex_Members optional 0 or greater EXAMPLE NEEDED  
10 DB_Xref(s) optional 0 or greater    
11 Gene_Product_Properties optional 0 or greater db_subset=Swiss-Prot  

Definitions and requirements for field contents

DB:DB_Object_ID

The DB prefix is the database abbreviation (namespace) from which the unique identifier DB Object ID is drawn and must be one of the values from the set of GO database cross-references. The DB:DB Object ID is the combined identifier for the database object. This field is mandatory, cardinality 1.\

DB_Object_Symbol

A (unique and valid) symbol to which the DB:DB_Object_ID is matched. No white spaces allowed.\ This field is mandatory, cardinality 1.\ The DB_Object_Symbol field should contain a symbol that is recognizable to a biologist wherever possible (an abbreviation widely used in the literature, for example). It is not a unique identifier or an accession number (unlike the DB:DB_Object_ID), although IDs can be used as a DB_Object_Symbol if there is no more biologically meaningful symbol available (e.g., when an unnamed gene is annotated). ORF names can be used for otherwise unnamed genes or proteins. If gene products are annotated, the gene product symbol can be used if available. Many gene product annotation entries may share a gene symbol. The text entered in the DB_Object_Symbol should refer to the entity in DB:DB_Object_ID. For example, several alternative transcripts from one gene may be annotated separately, each with specific gene product identifiers in DB:DB_Object_ID, but with the same gene symbol in the DB_Object_Symbol column.

DB_Object_Name

The name of the gene or gene product in DB:DB_Object_ID.\ This field is not mandatory, cardinality 0, 1 [white space allowed]\ The text entered in the DB_Object_Name and DB_Object_Symbol should refer to the entity in DB:DBB_Object_ID.

DB_Object_Synonym

These entries may be a gene symbol or other text. Note that we strongly recommend that synonyms are included in the GPI file, as this aids the searching of GO.\ This field is not mandatory, cardinality 0, 1, >1 [white space allowed]; for cardinality >1 use a pipe to separate entries (e.g. YFL039C|ABY1|END7|actin gene).

DB_Object_Type

An ontology identifier for the type of gene or gene product being annotated. This field uses Sequence Ontology, Protein Ontology, and GO labels and must correspond to one of the permitted GPI entity types or a more granular child term: SO:0001217 (protein-coding gene) ncRNA-coding gene ncRNA_gene SO:0001263 (ncRNA-coding gene) mRNA mRNA SO:0000234 (mRNA) ncRNA ncRNA SO:0000655 (ncRNA) protein protein PR:000000001 (protein) protein-containing complex protein-containing complex GO:0032991 (protein-containing complex)

marker or uncloned locus genetic_marker SO:0001645; or any subtype of ncRNA in the Sequence Ontology. If the precise product type is unknown, gene_product should be used.\ This field is mandatory, cardinality 1.\ The object type (gene, transcript, protein, protein_complex, etc.) listed in the DB_Object_Type field must match the database entry identified by the DB:DB_Object_ID. Note that DB_Object_Type refers to the database entry (i.e. it represents a protein, functional RNA, etc.); this column does not reflect anything about the GO term or the evidence on which the annotation is based.

DB Object Taxon

The NCBI taxon ID of the species encoding the gene product.\ This field is mandatory, cardinality 1.\ The taxon should be specified as a number with the prefix “taxon”.

Encoded by

For proteins and transcripts, Encoded by refers to the gene id that encodes those entities. This field is not mandatory, cardinality 0, 1, >1 ; for cardinality >1 use a pipe to separate entries.

Parent Protein CHANGE THIS TEXT

If the DB:DB_Object_ID refers to a variant of a gene product, this column will hold the identifier of the gene product from which it was derived.\ This field is mandatory, cardinality 1, when variant forms of a gene product (e.g. identifiers that specify distinct proteins produced by differential splicing, alternative translational starts, post-translational cleavage or post-translational modification) are represented in DB:DB_Object_ID. If the DB:DB_Object_ID refers to the canonical form of a gene product, this column should be blank.\ The identifier used must be a standard 2-part global identifier, e.g. UniProtKB:OK0206 The entity in the Parent_Object_ID column may not necessarily be the canonical form of the gene product; the canonical form would be identifiable as an entry for that gene product in the GPI file that would have the Parent_Object_ID blank.

Protein Containing Complex Members

DB_Xrefs

Identifiers for the object in DB:DB_Object_ID found in other databases.\ This field is optional, cardinality 0+; multiple identifiers should be pipe-separated.\ Identifiers used must be a standard 2-part global identifiers, e.g. UniProtKB:OK0206 This column should be used to record IDs for this object in other databases; for gene products in model organism databases, this must include the UniProtKB ID, and may also include NCBI gene or protein IDs, etc.

Gene Product Properties

This field is optional, cardinality 0+; multiple properties should be pipe-separated.\ The Properties column can be filled with a pipe separated list of values in the format “property_name = property_value”. There is a fixed vocabulary for the property names and this list can be extended when necessary. Supported properties will include: ‘GO annotation complete’, “Phenotype annotation complete’ (the value for these two properties would be a date), ‘Target set’ (e.g. Reference Genome, Kidney etc.), ‘Database subset’ (e.g. Swiss-Prot, TrEMBL).