Noctua - Upload of WB Manual Annotations
From WormBaseWiki
Jump to navigationJump to search- 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" (Note: an OA query for "NOT" didn't return any values, so I don't think we actually have any of these in the OA.) | NOT |
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. |
- Mapping qualifier names to RO ids.
qualifier name (gop_qualifier) | RO ID | |||
---|---|---|---|---|
part_of | BFO:0000050 | |||
enables | RO:0002327 | - | acts_upstream_of_or_within | RO:0002264 |
contributes_to | RO:0002326 | |||
located_in | RO:0001025 |