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

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| 01 || DB_Object_ID || required || 1 || 2 || Q4VCS5-1 || WBGene00000018
| 01 || DB_Object_ID || required || 1 || 2 || Q4VCS5-1 || WBGene00000035
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| 02 || DB_Object_Symbol || required || 1 || 3 || AMOT || abl-1
| 02 || DB_Object_Symbol || required || 1 || 3 || AMOT || ace-1
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|-
| 03 || DB_Object_Name || optional || 0 or 1 || 10 || Angiomotin ||  
| 03 || DB_Object_Name || optional || 0 or 1 || 10 || Angiomotin ||  
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|-
| 04 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || AMOT_HUMAN|KIAA1071|AMOT ||
| 04 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || AMOT_HUMAN|KIAA1071|AMOT || ACE1
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| 05 || DB_Object_Type || required || 1 || 12 || protein ||
| 05 || DB_Object_Type || required || 1 || 12 || protein || gene
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| 06 || Taxon || required || 1 || 13 || taxon:9606 || taxon:6239
| 06 || Taxon || required || 1 || 13 || taxon:9606 || taxon:6239
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| 07 || Annotation_Completed || optional || 1 || - || 20120614 || 20100405
| 07 || Annotation_Completed || optional || 1 || - || 20120614 (YYYYMMDD) || 20100405
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| 08 || Parent_Object_ID || optional || 0 or 1 || - || Q4VCS5 ||
| 08 || Parent_Object_ID || optional || 0 or 1 || - || Q4VCS5 || WBGene00000035
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| 09 || DB_Xref(s) || optional || 0 or greater || - || - || UniProtKB:Q4VCS5
| 09 || DB_Xref(s) || optional || 0 or greater || - || - || UniProtKB:P38433
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|}
|}

Revision as of 07:34, 22 November 2012

Link to previous proposed GPI format; http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Format

and previous proposed GPAD format; http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format

Issues for discussion:

gp_association files

Questions awaiting discussion with Chris;

  1. Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
  2. Filling in relationships retrospectively - implicit or explicit values in qualifier column?

Proposed format (21 Nov 2012)

contents required? cardinality old column # extra info
DB required 1 1 must be in xrf_abbs
DB_Object_ID required 1 2 canonical or spliceform ID
Qualifier optional 0 or greater 4 (NOT or integral_to)? (other_organism or colocalizes_with or contributes_to)? annotation_relation
GO ID required 1 5 must be extant GO ID
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

gp_information files

1. Have decided columns for DB_subset (e.g. Swiss-Prot, TrEMBL) and Annotation Target Set (e.g. Reference Genome) are not necessary.

2. Includes a column for Xrefs to other databases. 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.

3. It is proposed to dispose of Col.1 and replace it with a header line specifying the namespace of the annotating groups' identifiers, e.g. WB:, UniProtKB:?

None of the gp2protein files in the GOC SVN repository refer to objects from more than one namespace in column 1, so it seems like unnecessary repetition and redundancy to repeat the namespace in every row of the gpi file. Parent_object_id would only need to be qualified if it referred to an object from a different namespace (this could happen if we start annotating protein complexes)

Proposed format (21 Nov 2012)

column name required? cardinality GAF column Example for UniProt Example for WormBase
01 DB_Object_ID required 1 2 Q4VCS5-1 WBGene00000035
02 DB_Object_Symbol required 1 3 AMOT ace-1
03 DB_Object_Name optional 0 or 1 10 Angiomotin
04 DB_Object_Synonym(s) optional 0 or greater 11 KIAA1071|AMOT ACE1
05 DB_Object_Type required 1 12 protein gene
06 Taxon required 1 13 taxon:9606 taxon:6239
07 Annotation_Completed optional 1 - 20120614 (YYYYMMDD) 20100405
08 Parent_Object_ID optional 0 or 1 - Q4VCS5 WBGene00000035
09 DB_Xref(s) optional 0 or greater - - UniProtKB:P38433