Oct 2012 Meeting to finalize GPAD specification (Archived)

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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

Link to final GPAD/GPI format; Final GPAD and GPI file format

gp_association files

Questions awaiting discussion with Chris;

  1. Translating existing qualifiers CONTRIBUTES_TO and COLOCALIZES_WITH into annotation relations (+ NOT?)
N.B. The first line in the gp_association file should be;

!gpa-version: 1.1

Proposed format (21 Nov 2012)

column name required? cardinality old column # extra info
1 DB required 1 1 must be in xrf_abbs
2 DB_Object_ID required 1 2 canonical or spliceform ID
3 Qualifier required 0 or greater 4 (NOT or integral_to)? (other_organism or colocalizes_with or contributes_to)? annotation_relation
4 GO ID required 1 5 must be extant GO ID
5 DB:Reference(s) required 1 or greater 6 DB must be in xrf_abbs
6 Evidence code required 1 7 from ECO
7 With (or) From optional 0 or greater 8
8 Interacting taxon ID (for multi-organism processes) optional 0 or 1 13 ncbi taxon ID
9 Date required 1 14 YYYYMMDD
10 Assigned_by required 1 15 from xrf_abbs
11 Annotation Extension optional 0 or greater 16
12 Annotation Properties optional 0 or greater See Note 1 below

Note 1. The Annotation Properties column can be filled with a pipe separated list of "property_name = property_value". There will be a fixed vocabulary for the property names and this list can be extended when necessary. The initial supported properties would be curator_name and annotation_identifier*, but can be extended to include e.g. curator_ID, modification_date, creation_date, annotation_notes...etc.

* curator_name and annotation_identifier will be useful for groups that are using Protein2GO for protein annotation who wish to maintain their annotations in their own database. These values can be used to keep track of individual annotations.

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 (Col. 9). 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 the 'DB' column (e.g. UniProt, WB) 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)

N.B. The first two lines in the gp_information file should be;

!gpi-version: 1.1

!namespace: <database>

Proposed format (21 Nov 2012)

column name required? cardinality GAF column Example for UniProt Example for WormBase
01 DB_Object_ID required 1 2/17 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
N.B. Where it is stated that a column can have one or greater values, 
e.g. 'with', DB_Object_Synonym(s), DB_Xref(s), the values should be given as a pipe-separated list.