Difference between revisions of "Noctua - Upload of WB Manual Annotations"

From WormBaseWiki
Jump to navigationJump to search
(Created page with "*[https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md GPAD/GPI 2.0 specs on github] *Mapping from gop_ postgres tables to GPAD 2.0 column: {| cel...")
 
m
Line 5: Line 5:
 
{| cellspacing="2" border="1"
 
{| cellspacing="2" border="1"
 
|-
 
|-
! gop_ table name
+
! gop_ postgres table name
 
! GPAD 2.0 column
 
! GPAD 2.0 column
 
! Action
 
! Action
Line 13: Line 13:
 
| gop_wbgene || 1 || Preface each value with WB: || WB:WBGene00006925
 
| gop_wbgene || 1 || Preface each value with WB: || WB:WBGene00006925
 
|-
 
|-
| Status || is_obsolete: || If tag is not present, Status should be set to Valid.  If tag is present, Status should be set to Obsolete.
+
| gop_qualifier || 2|| Add text string "NOT" || NOT (An OA query for "NOT" didn't return any values, so I don't think we actually have any of these in the OA.)
 
|-
 
|-
| Definition || def: || Add corresponding value including double quotes.  Omit information in brackets at the end of the definition.
+
| gop_qualifier || 3 || Map text value to Relations Ontology term id (see below). ||
 
|-
 
|-
 
| Name || name: || Add corresponding value in double quotes.
 
| Name || name: || Add corresponding value in double quotes.

Revision as of 19:14, 13 May 2020

  • Mapping from gop_ postgres tables to GPAD 2.0 column:
gop_ postgres table name GPAD 2.0 column Action Example
gop_wbgene 1 Preface each value with WB: WB:WBGene00006925
gop_qualifier 2 Add text string "NOT" NOT (An OA query for "NOT" didn't return any values, so I don't think we actually have any of these in the OA.)
gop_qualifier 3 Map text value to Relations Ontology term id (see below).
Name name: Add corresponding value in double quotes.
Broad, Exact, Narrow, or Related synonym: For each synonym, check text after double quotes to populate Broad, Exact, Narrow, or Related. For ?Text add value in double quotes. Ignore information in brackets. Note that a single GO term object can have multiple synonyms.
Type namespace: Make first letter upper case and add corresponding value.
Instance is_a: Take object Name (id:) and look for that value in the is_a: tag for all entries. Fill in .ace tag with corresponding id: from obo file in double quotes. Can have multiple values.
Component relationship: part_of In each relationship: part_of tag, look for Name. Fill in .ace tag with corresponding id: in double quotes. Can have multiple values.
Instance_of is_a: For Name, look at is_a tag. Fill in .ace with corresponding value(s) in double quotes. Can have multiple values.
Component_of relationship: part_of For Name, look at relationship: part_of. Fill in .ace with corresponding value(s) in double quotes. Can have multiple values.
Ancestor is_a: and relationship: part_of For each Name, look at is_a: and relationship: part_of. Fill in .ace with each corresponding value in double quotes. Then, for each value filled in, iterate and look at their is_a: and relationship: part_of. Continue to fill in .ace with corresponding value until the root node is reached, for which no is_a or relationship: part_of exists. Remove any redundant values from list.
Descendent is_a: and relationship: part_of For each is_a: and relationship: part_of, look for Name. If Name matches value in either tag, fill in .ace with corresponding id: in double qutoes. For each corresponding id:, iterate and look for id: in is_a: and relationship: part_of. Continue to iterate until each id: is no longer found in is_a: and relationship: part_of. Remove any redundant values from list.
Version In header, data-version: releases/YYYY-MM-DD Gene Ontology followed by value after 'data-version:' tag.