Gene Product Association Data (GPAD) Format (Archived): Difference between revisions
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NB: although the gp2protein files may contain IDs of unannotated gene products, this data does | 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. | ||
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==Technical requirements and impact on existing software== | ==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 | |||
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. | |||
==Another Other Business== | |||
===What's all this spliceforms / isoforms stuff about?=== | |||
Please see the [[ GAF Col17 GeneProducts | 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. | |||
=== | |||
[[Category:GAF]] [[Category:Annotation]] | [[Category:GAF]] [[Category:Annotation]] |
Revision as of 11:57, 20 October 2009
Proposal to split the information in the GAF files into two sets, association data and gene product data.
The reasons for doing this are as follows:
- 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 GAF 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.
Current Association File Format
Annotation information has a shaded background, gene product data is in blue text, and information 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
Proposal: remove gene product data from the association file, leaving just an identifier.
Associations
new format for storing annotations:
old column # | required? | contents | cardinality |
---|---|---|---|
1 | required | DB | 1 |
17 if present; else 2 | required | Spliceform ID OR DB_Object_ID | 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 |
13 | optional | Interacting taxon ID (for multi-organism processes) | 0 or 1 |
14 | required | Date | 1 |
15 | required | Assigned_by | 1 |
16 | optional | Annotation Cross Products | 0 or greater |
Gene Products
Gene product data would be stored in a separate file. It would consist of the following pieces of information:
old column # | required? | contents | cardinality |
---|---|---|---|
1 | required | DB | 1 |
2 | required | DB_Object_ID | 1 |
3 | required | DB_Object_Symbol | 1 |
10 | optional | DB_Object_Name | 0 or 1 |
11 | optional | DB_Object_Synonym(s) | 0 or greater |
12 | required | DB_Object_Type | 1 |
13 | required | taxon | 1 |
Any GPs with different spliceforms would also have the following data (see GAF Col17 GeneProducts for more about spliceforms):
old column # | required? | contents | cardinality |
---|---|---|---|
17 | required | Spliceform ID | 1 |
12 | required | Spliceform object type | 1 |
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.
Example
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 |
This is how it could look in the proposed new format.
Association data:
1
DB |
17 or 2
Spliceform ID OR DB Object ID |
4
Qualifier |
5
GO ID |
6
DB:Reference(s) |
7
Evidence code |
8
With (or) From |
9
Aspect |
13
Interacting taxon ID (for multi-organism processes) |
14
Date |
15
Assigned_by |
16
Annotation cross products |
---|---|---|---|---|---|---|---|---|---|---|---|
SGD | S000000296 | GO:0003993 | SGD_REF:S000047763 | IMP | F | 20010118 | SGD | ||||
SGD | S000000296 | GO:0006796 | SGD_REF:S000047115 | TAS | P | 20041220 | SGD | ||||
SGD | S000005370 | NOT | GO:0003963 | SGD_REF:S000039255 | IDA | F | 20020530 | SGD | |||
SGD | S000005370 | GO:0006406 | SGD_REF:S000069956 | IC | GO:0000346 | P | taxon:745953 | 20030221 | SGD | ||
SGD | S000005370 | GO:0046820 | SGD_REF:S000057703 | ISS | CGSC:pabA | F | taxon:2861 | 20030106 | SGD | ||
UniProtKB | Q4VCS5 | GO:0031410 | PMID:11257124 | IDA | C | 20051207 | UniProtKB | ||||
UniProtKB | Q4VCS5 | GO:0043532 | PMID:11257124 | IDA | F | 20051207 | UniProtKB | ||||
UniProtKB | Q4VCS5-1 | GO:0043116 | PMID:16043488 | IDA | P | 20051207 | UniProtKB | ||||
UniProtKB | Q4VCS5-1 | GO:0005515 | PMID:16043488 | IPI | UniProtKB:Q6RHR9-2 | F | 20051207 | UniProtKB | |||
UniProtKB | Q4VCS5-2 | GO:0043532 | PMID:16043488 | IDA | F | 20051207 | UniProtKB |
GP data (including possible data from gp2protein file):
1
DB |
2
DB_Object_ID |
3
DB_Object_Symbol |
10
DB_Object_Name |
11
DB_Object_Synonym(s) |
12
DB_Object_Type |
13
taxon |
n/a
Spliceform ID, spliceform type |
n/a
?? xref from gp2protein file ?? |
---|---|---|---|---|---|---|---|---|
SGD | S000000296 | PHO3 | acid phosphatase | YBR092C | gene | taxon:4932 | UniProt:NE92D8 | |
SGD | S000005370 | RCL1 | aminodeoxychorismate synthase | YOL010W | gene | taxon:4932 | UniProt:JN97D8 | |
UniProtKB | Q4VCS5 | AMOT_HUMAN | AMOT, KIAA1071: Angiomotin | IPI00163085 | protein | taxon:9606 | Q4VCS5-1, snoRNA | Q4VCS5-2, protein | UniProt:Q4VCS5 |
The representation of the spliceforms could be changed if it isn't clear enough.
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.
Another 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.