Final GPAD and GPI file format: Difference between revisions

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m (Created page with " ===gp_association files (GPAD)=== <pre> N.B. The first line in the gp_association file should be; !gpa-version: 1.1 </pre> ====Final format (09 Jan 2013)==== {| style="bac...")
 
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Moved to https://github.com/geneontology/go-annotation/tree/master/specs


===gp_association files (GPAD)===
[[Category:Software]]
 
<pre>
N.B. The first line in the gp_association file should be;
 
!gpa-version: 1.1
</pre>
 
 
====Final format (09 Jan 2013)====
 
 
{| style="background:#ccffff" border=1 cell-padding=5 cell-spacing=10
|-
! 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 || qualifiers to be confirmed
|-
| 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 ||
|}
 
'''Notes'''
 
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.
 
<nowiki>*</nowiki> 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 (GPI)===
 
 
<pre>
N.B. The first two lines in the gp_information file should be;
 
!gpi-version: 1.1
 
!namespace: <database>
 
There should be a header line specifying the namespace of the annotating groups' identifiers, e.g. WB:, UniProtKB:
 
</pre>
 
====Final format (09 Jan 2013)====
 
 
{| cellspacing="2" border="1"
|-
! 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 || AMOT_HUMAN|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
|-
|}
 
 
'''Notes'''
 
1. 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.
 
 
2. The DB_Xrefs column will 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.
 
[[Category:Meetings]]
[[Category:Specification]]
[[Category:GPAD]]

Latest revision as of 18:41, 6 March 2020