GO Annotation File Format 1.0 Guide

File header

All gene association files must start with a single line denoting the file format, as follows:

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

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Annotation File Fields

The flat file format comprises 15 tab-delimited fields; red text denotes required fields.

Fields in the annotation file

Column	Content	Required?	Cardinality	Example
1	DB	required	1	UniProtKB
2	DB Object ID	required	1	P12345
3	DB Object Symbol	required	1	PHO3
4	Qualifier	optional	0 or greater	NOT
5	GO ID	required	1	GO:0003993
6	DB:Reference (|DB:Reference)	required	1 or greater	SGD_REF:S000047763|PMID:2676709
7	Evidence Code	required	1	IMP
8	With (or) From	optional	0 or greater	GO:0000346
9	Aspect	required	1	F
10	DB Object Name	optional	0 or 1	acid phosphatase
11	DB Object Synonym (|Synonym)	optional	0 or greater	YBR092C
12	DB Object Type	required	1	gene
13	Taxon(|taxon)	required	1 or 2	taxon:4932
14	Date	required	1	20010118
15	Assigned By	required	1	SGD

Definitions and requirements for field contents

DB (column 1)

refers to the database from which the identifier in DB object ID (column 2) is drawn. This is not necessarily the group submitting the file. If a UniProtKB ID is the DB object ID (column 2), DB (column 1) should be UniProtKB.
must be one of the values from the set of GO database cross-references
this field is mandatory, cardinality 1

DB Object ID (column 2)

a unique identifier from the database in DB (column 1) for the item being annotated
this field is mandatory, cardinality 1

The DB object ID (column 2) is the identifier for the database object, which may or may not correspond exactly to what is described in a paper. For example, a paper describing a protein may support annotations to the gene encoding the protein (gene ID in DB object ID field) or annotations to a protein object (protein ID in DB object ID field).

DB Object Symbol (column 3)

a (unique and valid) symbol to which DB object ID is matched
can use ORF name for otherwise unnamed gene or protein
if gene products are annotated, can use gene product symbol if available, or many gene product annotation entries can share a gene symbol
this field is mandatory, cardinality 1

The DB Object Symbol field should be a symbol that means something to a biologist wherever possible (a gene symbol, for example). It is not an ID or an accession number (the second column, DB object ID, provides the unique identifier), 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).

Qualifier (column 4)

flags that modify the interpretation of an annotation
one (or more) of NOT, contributes_to, colocalizes_with
this field is not mandatory; cardinality 0, 1, >1; for cardinality >1 use a pipe to separate entries (e.g. NOT|contributes_to)

See also the documentation on qualifiers in the GO annotation guide

GO ID (column 5)

the GO identifier for the term attributed to the DB object ID
this field is mandatory, cardinality 1

DB:Reference (column 6)

one or more unique identifiers for a single source cited as an authority for the attribution of the GO ID to the DB object ID. This may be a literature reference or a database record. The syntax is DB:accession_number.
Note that only one reference can be cited on a single line in the gene association file. If a reference has identifiers in more than one database, multiple identifiers for that reference can be included on a single line. For example, if the reference is a published paper that has a PubMed ID, we strongly recommend that the PubMed ID be included, as well as an identifier within a model organism database. Note that if the model organism database has an identifier for the reference, that identifier should always be included, even if a PubMed ID is also used.
this field is mandatory, cardinality 1, >1; for cardinality >1 use a pipe to separate entries (e.g. SGD_REF:S000047763|PMID:2676709).

Evidence Code (column 7)

see the GO evidence code guide for the list of valid evidence codes for GO annotations
this field is mandatory, cardinality 1

With [or] From (column 8)

Also referred to as with, from or the with/from column

one of:

• DB:gene_symbol
• DB:gene_symbol[allele_symbol]
• DB:gene_id
• DB:protein_name
• DB:sequence_id
• GO:GO_id

this field is not mandatory overall, but is required for some evidence codes (see below and the evidence code documentation for details); cardinality 0, 1, >1; for cardinality >1 use a pipe to separate entries (e.g. CGSC:pabA|CGSC:pabB)

Note: This field is used to hold an additional identifier for annotations using certain evidence codes (IC, IEA, IGI, IPI, ISS). For example, it can identify another gene product to which the annotated gene product is similar (ISS) or interacts with (IPI). More information on the meaning of with or from column entries is available in the evidence code documentation entries for the relevant codes.

Cardinality = 0 is not recommended, but is permitted because cases can be found in literature where no database identifier can be found (e.g. physical interaction or sequence similarity to a protein, but no ID provided). Cardinality = 0 is not allowed for ISS annotations made after October 1, 2006. Annotations where evidence is IGI, IPI, or ISS and with cardinality = 0 should link to an explanation of why there is no entry in with. Cardinality may be >1 for any of the evidence codes that use with; for IPI and IGI cardinality >1 has a special meaning (see evidence documentation for more information). For cardinality >1 use a pipe to separate entries (e.g. FB:FBgn1111111|FB:FBgn2222222).

Note that a gene ID may be used in the with column for a IPI annotation, or for an ISS annotation based on amino acid sequence or protein structure similarity, if the database does not have identifiers for individual gene products. A gene ID may also be used if the cited reference provides enough information to determine which gene ID should be used, but not enough to establish which protein ID is correct.

'GO:GO_id' is used only when the evidence code is IC, and refers to the GO term(s) used as the basis of a curator inference. In these cases the entry in the 'DB:Reference' column will be that used to assign the GO term(s) from which the inference is made. This field is mandatory for evidence code IC.

The ID is usually an identifier for an individual entry in a database (such as a sequence ID, gene ID, GO ID, etc.). Identifiers from the Center for Biological Sequence Analysis (CBS), however, represent tools used to find homology or sequence similarity; these identifiers can be used in the with column for ISS annotations.

The with column may not be used with the evidence codes IDA, TAS, NAS, or ND.

Aspect (column 9)

refers to the namespace or ontology to which the GO ID (column 5) belongs; one of P (biological process), F (molecular function) or C (cellular component)
this field is mandatory; cardinality 1

DB Object Name (column 10)

name of gene or gene product
this field is not mandatory, cardinality 0, 1 [white space allowed]

DB Object Synonym (column 11)

Gene symbol [or other text]
Note that we strongly recommend that gene synonyms are included in the gene association 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 (column 12)

what kind of thing is being annotated
one of gene (SO:0000704), transcript (SO:0000673), protein (SO:0000358), protein_structure, complex
this field is mandatory, cardinality 1

The object type (gene, transcript, protein, protein_structure, etc.) listed in the DB object type field must match the database entry identified by 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. For example, if your database entry represents a gene, then gene goes in the DB object type column, even if the annotation is to a component term relevant to the localization of a protein product of the gene. The text entered in the DB object name and DB object symbol can refer to the same database entry (recommended), or to a "broader" entity. For example, several alternative transcripts from one gene may be annotated separately, each with a unique transcript DB object ID, but list the same gene symbol in the DB object symbol column.

Taxon (column 13)

taxonomic identifier(s)
For cardinality 1, the ID of the species encoding the gene product.
For cardinality 2, to be used only in conjunction with terms that have the biological process term multi-organism process or the cellular component term host cell as an ancestor. The first taxon ID should be that of the organism encoding the gene or gene product, and the taxon ID after the pipe should be that of the other organism in the interaction.
this field is mandatory, cardinality 1, 2; for cardinality 2 use a pipe to separate entries (e.g. taxon:1|taxon:1000)
See the GO annotation conventions for more information on multi-organism terms.

Date (column 14)

Date on which the annotation was made; format is YYYYMMDD
this field is mandatory, cardinality 1

Assigned By (column 15)

The database which made the annotation
one of the values from the set of GO database cross-references
Used for tracking the source of an individual annotation.
Default value is value entered as the DB (column 1).
Value will differ from column 1 for any annotation that is made by one database and incorporated into another.
this field is mandatory, cardinality 1

Note that several fields contain database cross-reference (dbxrefs) in the format dbname:dbaccession. The fields are: GO ID [column 5], where dbname is always GO; DB:Reference (column 6); With or From (column 8); and Taxon (column 13), where dbname is always taxon. For GO IDs, do not repeat the 'GO:' prefix (i.e. always use GO:0000000, not GO:GO:0000000)

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