Oct 2012 Meeting to finalize GPAD specification (Archived): Difference between revisions

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Issues for discussion:
Issues for discussion:


===gp_association files===
#Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
#Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
#Filling in relationships retrospectively - implicit or explicit values in column 4?  
#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. Also, it does not contain xrefs to other databases.
{| cellspacing="2" border="1"
|-
! 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
|-
| 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 || AMOT|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 || - || BHF-UCL|KRUK|Reference Genome
|-
| 10 || Annotation_Completed || optional || 1 || - || timestamp (YYYYMMDD)
|-
| 11 || Parent_Object_ID || optional || 0 or 1 || - || UniProtKB:P21677
|-
|}


[[Category:Meetings]]
[[Category:Meetings]]
[[Category:Specification]]
[[Category:Specification]]
[[Category:GPAD]]
[[Category:GPAD]]

Revision as of 04:03, 17 October 2012

Issues for discussion:

gp_association files

  1. Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
  2. Filling in relationships retrospectively - implicit or explicit values in column 4?
  3. 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. Also, it does not contain xrefs to other databases.

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
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
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