About GPAD/GPI files

The Gene Ontology Consortium stores annotation data, the representation of gene product attributes using GO terms, in tab-delimited text files. Gene Product Association Data (GPAD) and (Gene Product Information) (GPI) companion files reduce the redundancy of the Gene Association File (GAF). GAF files contains information about gene products that are present in each line of the GAF: each non-header line in an annotation 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. The GPAD/GPI file system normalizes the data by separating the annotations and metadata about gene and gene product entities in two separate files. GPAD/GPI is intended for internal GO use.

GO also provides annotations as GAF files and recommends use of the GAF format for most use cases. For more general information on annotation, please see the Introduction to GO annotation.

Gene Product Information (GPI) 2.0 file guidelines

This page is a summary of the Gene Product Information Data (GPI) 2.0 format; for full technical details and changes from GPI 1.2 see the GitHub specification page. Note that the GPI file is the companion file for the GPAD file. Both files should be submitted together using the same version.

Changes from the GPI 1.2 to GPI 2.0

Characters allowed in all fields have been explicitly specified
Extensions in file names are: *.gpad and *.gpi

Header

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

Columns

Columns 1 & 2 in 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

GPI Header

All annotation files MUST start with a single line denoting the file format. The database/group generating the file, as listed in dbxrefs.yaml, and the ISO-8601 formatted date the file was generated MUST also be included in the header. Example for GPI 2.0:

!gpi-version: 2.0
!generated-by: SGD 
!date-generated: 2024-05-01

The group in the generated-by field must be present in the dbxrefs.yaml file. The year must be YYYY-MM-DD, conforming to the date portion of ISO 8601 standards. Submitting groups may choose to include optional additional information in a file header by prefixing the line with an exclamation mark (!); such lines will be ignored by parsers. For example:

!URL: http://www.yeastgenome.org/
!Project-release: WS275
!Funding: NHGRI grant number HG012212
!go-version: https://doi.org/10.5281/zenodo.8436609

GPI file fields

The file format comprises 11 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:Q4VCS5-1
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	KIAA1071
5	DB_Object_Type	required	1	PR:000000001
6	DB_Object_Taxon	required	1	NCBITaxon:9606
7	Encoded_by	optional	0 or greater	HGNC:17810
8	Parent_Protein	optional	0 or 1	UniProtKB:Q4VCS5
9	Protein_Containing_Complex_Members	optional	0 or greater	SGD:S000003821\|SGD:S000001456\|SGD:S000005047
10	DB_Xref(s)	optional	0 or greater	NCBIGene:154796\|ENSEMBL:ENSG00000126016
11	Gene_Product_Properties	optional	0 or greater	db_subset=Swiss-Prot

GPI 2.0 example content

SGD:S000005027  Sal1  ADP/ATP transporter  YNL083W  PR:000000001  NCBITaxon:559292    UniProtKB:D6W196

Complex:

SGD:S000217643  CBF1:MET4:MET28 sulfur metabolism transcription factor complex    GO:0032991  NCBITaxon:559292      SGD:S000003821,SGD:S000001456,SGD:S000005047  ComplexPortal:CPX-1016

ncRNA:

RNAcentral:URS0000527F89_9606		Homo sapiens (human) hsa-miR-145-5p    SO:0000276		NCBITaxon:9606  HGNC:31532      NCBIGene:406937|ENSEMBL:ENSG00000276365

Definitions and requirements for field contents

1. DB:DB Object ID

A unique identifier for the item being annotated. The DB prefix is the database from which the 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. Examples:

UniProtKB:P99999
SGD:S000002164
MGI:MGI:1919306

The identifier usually references the canonical form of a gene or gene product including functional RNAs. Identifiers may also describe gene variants, distinct proteins produced by to differential splicing, alternative translational starts, post-translational cleavage or post-translational modification. If the gene product is not a canonical gene or gene product identifier, the Gene Product Information (GPI) file should contain information about the canonical form of the gene or gene product.

This field is mandatory, cardinality 1.

2. DB Object Symbol

A (unique and valid) symbol to which the DB:DB_Object_ID is matched. No white spaces allowed.

The text entered in the DB_Object_Symbol should refer to the entity in DB:DB_Object_ID. The DB_Object_Symbol field should contain a symbol that is recognizable to a biologist wherever possible (gene product symbol, abbreviation widely used in the literature, ORF name, etc.). 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). 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.

This field is mandatory, cardinality 1.

3. DB Object Name

The name of the gene or gene product in DB:DB_Object_ID. The text entered in the DB_Object_Name should refer to the entity in DB:DB_Object_ID. White spaces are allowed in this field.

This field is not mandatory, cardinality 0, 1.

4. DB Object Synonym

Alternative names for the entity in DB:DB_Object_ID. 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).

5. DB Object Type

An ontology identifier for the biological entity in DB:DB_Object_ID which is annotated with GO. This field uses Sequence Ontology, Protein Ontology, and GO IDs and must correspond to one of the permitted GPI entity types or a more granular child term. Common entries include:

protein PR:000000001
protein-coding gene SO:0001217
gene SO:0000704
ncRNA SO:0000655
- any subtype of ncRNA in the Sequence Ontology, including ncRNA-coding gene SO:0001263
protein-containing complex GO:0032991

The object type listed in the DB_Object_Type field must match the database entry identified by the DB:DB_Object_ID.

This field is mandatory, cardinality 1.

6. DB Object Taxon

The NCBI taxon ID of the species encoding the DB:DB_Object_ID, including the prefix NCBITaxon:.

This field is mandatory, cardinality 1.

7. Encoded by

For proteins and transcripts, Encoded by refers to the gene ID that encodes those entities, e.g. ENSG00000197153.