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

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| gop_wbgene || 1 || Preface each value with WB: || WB:WBGene00006925
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| 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
 
|-
 
|-
| gop_paper || 5 || Pipe separate PMID and WBPaper ID || PMID:10978280|WB:WBPaper00004310
+
| gop_accession || 5 || Add id as it exists in table. || GO_REF:0000015
 +
|-
 +
| gop_paper || 5 || Add WBPaper ID and corresponding PMID, 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_goinference || 6 || Map three-letter GO code to ECO code (see below); add ECO id. || ECO:0000314
 
|-
 
|-
| 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.
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| gop_with_wbgene || 7 || Preface each value with 'WB:'; comma-separate multiple values || WB:WBGene00000001
 +
|-
 +
| gop_with || 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_wbvariation || 7 || Preface each value with 'WB:'; comma-separate multiple values || WB:WBVar00242156
 +
|-
 +
| ?? || 8 || Not sure if we have any values for an interacting taxon. || ??
 
|-
 
|-
| Component || relationship: part_of || In each relationship: part_of tag, look for NameFill in .ace tag with corresponding id: in double quotes.  Can have multiple values.
+
| gop_lastupdate || 9 || If YYYY-MM-DD, add as exists in tableIf YYYY-MM-DD HH:MM:SS convert to: YYYY-MM-DDTHH:MM || 2020-05-13 or 2006-02-03T12:26
 
|-
 
|-
| 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.
+
| no OA table || 10 || Add WB || WB
 
|-
 
|-
| 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.
+
| gop_xrefto || 11 || Convert relation name to RO id, add parenthetical value. || RO:0002233(WB:WBGene00000584)
|-
 
| 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.
+
| ?? || 12 || Add postgres annotation id, prefixed with 'id=WBOA:' || id=WBOA:3565
 
|-
 
|-
| Version || In header, data-version: releases/YYYY-MM-DD || Gene Ontology followed by value after 'data-version:' tag.
+
| gop_curator || 12 || If available, map curator to ORCID and prefix with 'contributor-id=https://orcid.org/'.  If no ORICD, add 'GOC:cab1' || contributor-id=https://orcid.org/0000-0002-1478-7671
 +
|-
 +
| gop_comment || 12 || Add free text, prefixed with 'comment=' || comment=2020-03-17; flagged FP prior to Noctua upload; no ISS With/From; more specific PAINT annotation exists.
 
|-
 
|-
 
|}
 
|}
  
= Mapping qualifier names to RO ids. =
+
= Mapping relation names to RO ids. =
  
 
{| cellspacing="2" border="1"
 
{| cellspacing="2" border="1"
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|-
 
|-
 
| contributes_to || RO:0002326
 
| contributes_to || RO:0002326
 +
|-
 +
| has_input || RO:0002233
 +
|-
 +
| happens_during || RO:0002092
 
|-
 
|-
 
|}
 
|}
 
  
 
= Mapping three-letter GO codes to ECO ids. =
 
= Mapping three-letter GO codes to ECO ids. =

Revision as of 15:42, 18 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
gop_accession 5 Add id as it exists in table. GO_REF:0000015
gop_paper 5 Add WBPaper ID and corresponding PMID, 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_wbgene 7 Preface each value with 'WB:'; comma-separate multiple values WB:WBGene00000001
gop_with 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_wbvariation 7 Preface each value with 'WB:'; comma-separate multiple values WB:WBVar00242156
?? 8 Not sure if we have any values for an interacting taxon. ??
gop_lastupdate 9 If YYYY-MM-DD, add as exists in table. If YYYY-MM-DD HH:MM:SS convert to: YYYY-MM-DDTHH:MM 2020-05-13 or 2006-02-03T12:26
no OA table 10 Add WB WB
gop_xrefto 11 Convert relation name to RO id, add parenthetical value. RO:0002233(WB:WBGene00000584)
?? 12 Add postgres annotation id, prefixed with 'id=WBOA:' id=WBOA:3565
gop_curator 12 If available, map curator to ORCID and prefix with 'contributor-id=https://orcid.org/'. If no ORICD, add 'GOC:cab1' contributor-id=https://orcid.org/0000-0002-1478-7671
gop_comment 12 Add free text, prefixed with 'comment=' comment=2020-03-17; flagged FP prior to Noctua upload; no ISS With/From; more specific PAINT annotation exists.

Mapping relation 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
has_input RO:0002233
happens_during RO:0002092

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?