Oct 2012 Meeting to finalize GPAD specification (Archived): Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
|||
Line 1: | Line 1: | ||
Link to previous proposed format; http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Format | Link to previous proposed format; http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Format | ||
and here; http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format | |||
Issues for discussion: | Issues for discussion: |
Revision as of 07:43, 24 October 2012
Link to previous proposed format; http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Format and here; http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format
Issues for discussion:
gp_association files
- Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
- Filling in relationships retrospectively - implicit or explicit values in column 4?
- spliceforms - separate column with canonical form in column 2 as per GAF, or column 2 only?
gp_information files
gp_information.goa_uniprot (gpi-version: 1.0) currently has these columns, some of which (db_subset, annotation_target_set, annotation_completed) are not present in the proposed 1.1 format.
It does not contain xrefs to other databases, however this would be useful for mapping of MOD-specific identifiers/symbols/synonyms to UniProt accessions to assist MOD curators moving to Protein2GO in searching for familiar IDs/gene names.
column | name | required? | cardinality | GAF column | Example |
---|---|---|---|---|---|
01 | DB | required | 1 | 1 | UniProtKB |
02 | DB_Subset | optional | 0 or 1 | - | Swiss-Prot or TrEMBL |
03 | DB_Object_ID | required | 1 | 2 | Q4VCS5-1 |
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:Q4VCS5 |