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

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| 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 || 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  
 
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| gop_qualifier || 3 || Map text value to Relations Ontology term id (see below). ||  
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| gop_qualifier || 3 || Map text value to Relations Ontology (RO) term id (see below); add RO id. || RO:0001025
 
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| Name || name: || Add corresponding value in double quotes.
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| gop_goid || 4|| Add GO term id. || GO:0051306
 
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| 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.  
 
| 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.  
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= Mapping qualifier names to RO ids. =
 
= Mapping qualifier names to RO ids. =

Revision as of 20:32, 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" (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 (RO) term id (see below); add RO id. RO:0001025
gop_goid 4 Add GO term id. GO:0051306
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
colocalizes_with RO:0002325
involved_in RO:0002331
located_in RO:0001025
contributes_to RO:0002326

Questions

  • What about blank OA entries, e.g. pgid 14222?