Gene Product Association Data (GPAD) Format (Archived)

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An alternative means of exchanging annotations. The GPAD format is designed to be more normalized than GAF, and is intended to work in conjunction with a separate format for exchanging gene product information.


In Brief...

This proposal separates data on genes and gene products, objects being annotated, from the annotation data. The data related to gene products--symbol, name, synonyms, taxon--can be submitted, updated and maintained separately from that concerned with annotation: term IDs, evidence codes, references, annotation extension (col 16), and so on.

Additionally, we would like to introduce further flexibility in annotation by using the entire suite of evidence codes available in the Evidence Code Ontology and standardization of the types of object (gene product types) that can be annotated. A controlled vocabulary has not yet been introduced for the latter.


Why?

  • allow unannotated gene products to be submitted to the GO database
    • could be useful in estimating the proportion of a genome that has been annotated
    • will also allow users to see that the GP they are searching for does exist, so they won't spend a long time fruitlessly searching for it [see note below]
  • reduce the amount of redundant gene product information in the GAF files
    • every annotation to a gene product repeats the same gene product data; this only needs to be stated once. Removing this repeated information and supplying it in a separate file will mean the annotation data files will be smaller, which would certainly be helpful for huge files like the UniProt releases.

NB: although the gp2protein files may contain IDs of unannotated gene products, this data does not go into the GO database, and it is not available in AmiGO. There is also no information available about gene product name, synonyms, type or taxon of unannotated gene products in the gp2protein file or in the GAF files.


How?

  • Converting a GAF file into the GP information and annotation data files, and vice versa, would be simple enough that groups submitting data will be able to provide it in either format, and data consumers will be able to download it in GAF or the proposed formats.

See Technical requirements and impact on existing software for more details.


Current Association File Format

File Header

The gene association file begins with a line declaring the format version as follows:

!gaf-version: 2.0

Any comments or information should be preceded by an exclamation mark, indicating that parsers should ignore that line. An example of a full file header could look like this:

!gaf-version: 2.0
!CVS Version: Revision: 1.134 $
!GOC Validation Date: 08/26/2009 $
!Submission Date: 8/26/2009
!
! The above "Submission Date" is when the annotation project provided
! this file to the Gene Ontology Consortium (GOC).  The "GOC Validation
! Date" indicates when this file was last changed as a result of a GOC
! validation and filtering process.  The "CVS Version" above is the
! GOC version of this file.
!
!
!Project_name: Schizosaccharomyces pombe GeneDB
!URL: www.genedb.org/genedb/pombe
!Contact Email: val@sanger.ac.uk
!

File Body

Annotation data has a shaded background, gene product information is in blue text, and data required for both has blue text on a shaded background.

column required? contents cardinality
1 required DB 1
2 required DB_Object_ID 1
3 required DB_Object_Symbol 1
4 optional Qualifier 0 or greater
5 required GO ID 1
6 required DB:Reference(s) 1 or greater
7 required Evidence code 1
8 optional With (or) From 0 or greater
9 required Aspect 1
10 optional DB_Object_Name 0 or 1
11 optional DB_Object_Synonym(s) 0 or greater
12 required DB_Object_Type (refers to col 17 if present) 1
13 required taxon 1 or 2 (for multi-org processes)
14 required Date 1
15 required Assigned_by 1
16 optional Annotation cross products  ?
17 optional Spliceform 1

Proposed file format

Gene Product Association Data, GPAD

All gene product data barring the ID of the object being annotated is removed from the annotation file.

File Header

The file starts with a line declaring the file format:

!gpad-version: 1.0

Further information or remarks should be prefixed by an exclamation mark. An example of a full file header:

!gpad-version: 1.0
!CVS Version: Revision: 1.134 $
!GOC Validation Date: 08/26/2009 $
!Submission Date: 8/26/2009
!
! The above "Submission Date" is when the annotation project provided
! this file to the Gene Ontology Consortium (GOC).  The "GOC Validation
! Date" indicates when this file was last changed as a result of a GOC
! validation and filtering process.  The "CVS Version" above is the
! GOC version of this file.
!
!
!Project_name: Schizosaccharomyces pombe GeneDB
!URL: www.genedb.org/genedb/pombe
!Contact Email: val@sanger.ac.uk
!

File Body

contents required? cardinality old column # extra info
DB required 1 1 must be in xrf_abbs
DB_Object_ID required 1 2
Qualifier optional 0 or greater 4 'NOT' should not be in this column
(NOT) GO ID required 1 5 must be extant GO ID, prefixed with NOT for NOT associations
DB:Reference(s) required 1 or greater 6 DB must be in xrf_abbs
Evidence code required 1 7 from ECO
With (or) From optional 0 or greater 8
Interacting taxon ID (for multi-organism processes) optional 0 or 1 13 ncbi taxon ID
Date required 1 14 YYYYMMDD
Assigned_by required 1 15 from xrf_abbs
Annotation XP (Annotation Cross Products) optional 0 or greater 16

Note: NOT would be moved to the GO ID column. This makes it clearer when an annotation is negated and makes it much more difficult for 'NOT' to be ignored.

Additional Data

The addition of an annotation ID could be useful for a number of reasons, including updating, removing or citing annotations, linking different annotations, and so on. There are questions about how and by whom these IDs would be maintained that would need to be answered before introducing such IDs.

Gene Product Information

Gene product information is stored in a separate file.

File Header

The file starts with a line declaring the file format:

!gpi-version: 1.0

Further information or remarks should be prefixed by an exclamation mark:

!gpi-version: 2.0
!CVS Version: Revision: 1.134 $
!GOC Validation Date: 08/26/2009 $
!Submission Date: 8/26/2009
!
!Project_name: Schizosaccharomyces pombe GeneDB
!URL: www.genedb.org/genedb/pombe
!Contact Email: val@sanger.ac.uk
!

File Body

contents required? cardinality GAF 2.0 col # extra info
DB required 1 1 in xrf_abbs
DB Object ID required 1 2
DB Object Type required 1 12 need a controlled vocab (SO + GO complex? PRO?)
Taxon required 1 13
DB Object Symbol required 1 3
DB Object Name optional 0 or 1 10
DB Object Synonym(s) optional 0 or greater 11
Parent GP ID blank unless GP is an isoform (see next table) 0 n/a protein - list gene; complex component - list complex ID
Xrefs in other DBs (e.g. xrefs from gp2protein or the QFO file) optional 0+, pipe-separated n/a


  • check PRO for examples
  • should we have a richer way to represent relationships between genes and the various types of gene product and GP complexes?

Spliceforms (see GAF Col17 GeneProducts for more about spliceforms) would have their own entries in this file, with the data as follows:

contents required? cardinality GAF 2.0 col #
DB required 1 1
DB Object ID required 1 17
DB Object Type required 1 12
Taxon required 1 13
DB Object Symbol required 1 3
DB Object Name optional 0 or 1 10
DB Object Synonym(s) optional 0 or greater 11
Parent GP ID required 1 2
Xrefs in other DBs (e.g. xrefs from gp2protein or the QFO file) optional 0+, pipe-separated n/a


Multiple entries in the xrefs col should be pipe-separated.

Ideally, the gene product files would also include the gp2protein data, so we would have an additional piece of data, an xref to a UniProt or NCBI ID.

Additional Data

Extra information can be included in the GPI files, including whether annotation is complete for a certain GP, and whether that GP belongs to a set prioritized for annotation. See GOA comment below.

Example

Old GAF 1.0 Format

The following appears on the page http://geneontology.org/GO.annotation.fields.shtml and is an example of the current GAF file structure (shaded bg: annotation data; blue text: gp data):

1

DB

2

DB Object ID

3

DB Object Symbol

4

Qualifier

5

GO ID

6

DB:Reference(s)

7

Evidence code

8

With (or) From

9

Aspect

10

DB Object Name

11

DB Object Synonym(s)

12

DB Object Type (refers to col 17 if present)

13

taxon

14

Date

15

Assigned by

16

Annotation cross products

17

Spliceform

SGD S000000296 PHO3 GO:0003993 SGD_REF:S000047763 IMP F acid phosphatase YBR092C gene taxon:4932 20010118 SGD
SGD S000000296 PHO3 GO:0006796 SGD_REF:S000047115 TAS P acid phosphatase YBR092C gene taxon:4932 20041220 SGD
SGD S000005370 RCL1 NOT GO:0003963 SGD_REF:S000039255 IDA F aminodeoxychorismate synthase YOL010W gene taxon:4932 20020530 SGD
SGD S000005370 RCL1 GO:0006406 SGD_REF:S000069956 IC GO:0000346 P aminodeoxychorismate synthase YOL010W gene taxon:4932|taxon:745953 20030221 SGD
SGD S000005370 RCL1 GO:0046820 SGD_REF:S000057703 ISS CGSC:pabA F aminodeoxychorismate synthase YOL010W gene taxon:4932|taxon:2861 20030106 SGD
UniProtKB Q4VCS5 AMOT_HUMAN GO:0031410 PMID:11257124 IDA C AMOT, KIAA1071: Angiomotin IPI00163085 protein taxon:9606 20051207 UniProtKB
UniProtKB Q4VCS5 AMOT_HUMAN GO:0043532 PMID:11257124 IDA F AMOT, KIAA1071: Angiomotin IPI00163085 protein taxon:9606 20051207 UniProtKB
UniProtKB Q4VCS5 AMOT_HUMAN GO:0043116 PMID:16043488 IDA P AMOT, KIAA1071:Angiomotin IPI00163085 snoRNA taxon:9606 20051207 UniProtKB Q4VCS5-1
UniProtKB Q4VCS5 AMOT_HUMAN GO:0005515 PMID:16043488 IPI UniProtKB:Q6RHR9-2 F AMOT, KIAA1071: Angiomotin IPI00163085 snoRNA taxon:9606 20051207 UniProtKB Q4VCS5-1
UniProtKB Q4VCS5 AMOT_HUMAN GO:0043532 PMID:16043488 IDA F AMOT, KIAA1071: Angiomotin IPI00163085 protein taxon:9606 20051207 UniProtKB Q4VCS5-2


Proposed new format

This is how it could look in the proposed new format.

Association data:

DB DB Object ID Qualifier GO ID DB:Reference(s) Evidence code With (or) From Interacting taxon ID (for multi-organism processes) Date Assigned_by Annotation cross products Spliceform ID (if applicable)
SGD S000000296 GO:0003993 SGD_REF:S000047763 ECO:0000015 20010118 SGD
SGD S000000296 GO:0006796 SGD_REF:S000047115 ECO:0000304 20041220 SGD
SGD S000005370 NOT GO:0003963 SGD_REF:S000039255 ECO:0000002 20020530 SGD
SGD S000005370 GO:0006406 SGD_REF:S000069956 ECO:0000305 GO:0000346 taxon:745953 20030221 SGD
SGD S000005370 GO:0046820 SGD_REF:S000057703 ECO:0000250 CGSC:pabA taxon:2861 20030106 SGD
UniProtKB Q4VCS5 GO:0031410 PMID:11257124 ECO:0000002 20051207 UniProtKB
UniProtKB Q4VCS5 GO:0043532 PMID:11257124 ECO:0000002 20051207 UniProtKB
UniProtKB Q4VCS5 GO:0043116 PMID:16043488 ECO:0000002 20051207 UniProtKB Q4VCS5-1
UniProtKB Q4VCS5 GO:0005515 PMID:16043488 ECO:0000021 UniProtKB:Q6RHR9-2 20051207 UniProtKB Q4VCS5-1
UniProtKB Q4VCS5-2 GO:0043532 PMID:16043488 ECO:0000002 20051207 UniProtKB Q4VCS5-2


Gene Product Information (including possible data from gp2protein file) -- see the gene product information file format for an in-depth view.

DB DB_Object_ID DB_Object_Type Taxon DB Object Symbol DB Object Name DB Object Synonym(s) Parent GP ID Xrefs in other DBs
SGD S000000296 gene 4932 PHO3 acid phosphatase YBR092C UniProt:NE92D8
SGD S000005370 gene 4932 RCL1 aminodeoxychorismate synthase YOL010W UniProt:JN97D8
UniProtKB Q4VCS5 protein 9606 AMOT_HUMAN AMOT, KIAA1071: Angiomotin KIAA1071
UniProtKB Q4VCS5-1 snoRNA 9606 AMOT_HUMAN Isoform 1 of Angiomotin UniProtKB:Q4VCS5
UniProtKB Q4VCS5-2 protein 9606 AMOT_HUMAN Isoform 2 of Angiomotin UniProtKB:Q4VCS5

Technical requirements and impact on existing software

For the most part, the changes suggested are simply a split of existing GAF files into two separate files, with a rearrangement of existing columns. It would be fairly easy to write a standalone script that could take in the two files and produce one from them, or vice versa.


GO Database

Some modifications of the database loading scripts would need to be made; the new formats mirror the database structure more closely so it should actually be an improvement.


Groups submitting GO data

Rather than writing out a single GAF file, two will be required: a file containing gene product data, and a file containing annotations. For databases with a GO database-like schema, where annotation information and gene product data are kept in separate tables, this new format will more closely mirror database structure.


Groups using GO data

There are two options here; either we provide files in all formats, or we provide files in one format and supply users with a script to convert the data. The latter would incur less cost in terms of processing time and storage space for the GOC. A gradual transition to using the new format and a period of supplying both old and new files (as was done with the ontology files) is probably the best option.


Any Other Business

What's all this spliceforms / isoforms stuff about?

Please see the documentation on column 17 for more details. Although the proposal for col 17 has been accepted by the GO Consortium, it is not clear how many databases are annotating different isoforms and are hence using col 17.

Comments

GOA: This file is a great idea. We feel that it would greatly benefit our users. However could we extend the proposed format of this file further, to additionally include optional attribute-value pairs that describe:


1. DB subset (for GOA this would have values either Swiss-Prot or TrEMBL)

2. Target set member (to indicate if a protein has been prioritized by an annotation project, such as Reference Genomes, the Renal or Cardiovascular annotation projects). This would mean curators could move away from having to fill in multiple Reference Genomes google spreadsheets.

3. Annotation Complete: yes/no (annotation data all groups now store such information, but there is no current export mechanism for this data)

(Edimmer 11:27, 26 January 2010 (UTC))

The UniProt gp_association and gp_information files

Since June 2010 GOA has been supplying the UniProt annotation set in gp_association and gp_information files, in addition to the (GAF2.0 format) gene_association file; they can be found at gp_association.goa_uniprot.gz and gp_information.goa_uniprot.gz.

The format of these files is fully documented in gp_association_readme and gp_information_readme, but, in summary, the columns present in each of the files are as follows:

gp_association

column name required? cardinality GAF column
01 DB required 1 1
02 DB_Object_ID required 1 2
03 Qualifier optional 0 or greater 4
04 GO ID required 1 5
05 DB:Reference(s) required 1 or greater 6
06 Evidence code required 1 7
07 With optional 0 or greater 8
08 Extra taxon ID optional 0 or 1 13
09 Date required 1 14
10 Assigned_by required 1 15
11 Annotation Extension optional 0 or greater 16
12 Spliceform ID optional 0 or 1 17

gp_information

column name required? cardinality GAF column Example content
01 DB required 1 1 UniProtKB
02 DB_Subset optional 0 or 1 - Swiss-Prot or TrEMBL
03 DB_Object_ID required 1 2 Q4VCS5
04 DB_Object_Symbol required 1 3 AMOT
05 DB_Object_Name optional 0 or 1 10 Angiomotin
06 DB_Object_Synonym(s) optional 0 or greater 11 KIAA1071|IPI:IPI00163085|IPI:IPI00644547|UniProtKB:AMOT_HUMAN
07 DB_Object_Type required 1 12 protein
08 Taxon required 1 13 taxon:9606
09 Annotation_Target_Set optional 0 or greater - KRUK|Reference Genome
10 Annotation_Completed optional 1 - timestamp (YYYYMMDD)
11 Parent_Object_ID optional 0 or 1 - UniProtKB:P21677