Difference between revisions of "Noctua - Upload of WB Manual Annotations"
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− | | gop_wbgene || 1 || Preface each value with WB: || WB:WBGene00006925 | + | | 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 || 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_goid || 4|| Add GO term id. || GO:0051306 | | gop_goid || 4|| Add GO term id. || GO:0051306 | ||
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− | | gop_paper || 5 || | + | | gop_paper || 5 || Add PMID and WBPaper ID, pipe separated. || PMID:10978280|WB:WBPaper00004310 |
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| gop_goinference || 6 || Map three-letter GO code to ECO code (see below); add ECO id. || ECO:0000314 | | 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 |
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− | | | + | | 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. | | 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. | ||
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Revision as of 14:22, 18 May 2020
Contents
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?