Noctua - Upload of WB Manual Annotations

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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
gop_paper 5 Add PMID and WBPaper ID, pipe separated. PMID:10978280|WB:WBPaper00004310
gop_goinference 6 Map three-letter GO code to ECO code (see below); add ECO id. ECO:0000314
gop_with_gene 7 Preface each value with 'WB:'; comma-separate multiple values WB:WBGene00000001
gop_with_other 7 Add id as it exists in table; comma-separate multiple values FB:FBgn0003719
gop_with_phenotype 7 Add id as it exists in table; comma-separate multiple values WBPhenotype:0000689
gop_with_rnai 7 Preface each value with 'WB:'; comma-separate multiple values WB:WBRNAi00001974
gop_with_variation 7 Preface each value with 'WB:'; comma-separate multiple values WB:WBVar00242156
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


Mapping three-letter GO codes to ECO ids.

three-letter GO code ECO ID
ISS ECO:0000250
IEP ECO:0000270
NAS ECO:0000303
TAS ECO:0000304
IC ECO:0000305
ND ECO:0000307
IDA ECO:0000314
IMP ECO:0000315
IGI ECO:0000316
IPI ECO:0000353

Questions

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