Difference between revisions of "Relations Ontology"

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(Created page with "= Parsing Scripts for ?RO_term Model and ?GO_annotation models = ?RO_term .ace parsing script (See /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_...")
 
m
Line 21: Line 21:
  
 
Fields to include, mapped to ?RO_term model tag (note that we can re-use much of the ?GO_term parsing script):
 
Fields to include, mapped to ?RO_term model tag (note that we can re-use much of the ?GO_term parsing script):
Id: -> RO_term
+
*Id: -> RO_term
Name: -> Name
+
*Name: -> Name
Status -> Valid
+
*Status -> Valid
alt_id: -> Alt_id
+
*alt_id: -> Alt_id
Def: -> Definition (parse what is in quotes)
+
*Def: -> Definition (parse what is in quotes)
Synonym: -> Synonym (parse what is in caps to match Type and then the text that is in quotes
+
*Synonym: -> Synonym (parse what is in caps to match Type and then the text that is in quotes
Data-version: -> Version
+
*Data-version: -> Version
  
 
Review GO term parser for handling is_a relationships to populate Child, Parent, Index
 
Review GO term parser for handling is_a relationships to populate Child, Parent, Index
***Update spelling of Descendant in ?GO_term model***
 
  
 
Parsing report/sanity check:
 
Parsing report/sanity check:
Line 36: Line 35:
 
What terms have no descendants?
 
What terms have no descendants?
  
go_gpad_parser modifications
+
=Update spelling of Descendant in ?GO_term model =
 +
 
 +
= go_gpad_parser modifications =
 
/home/acedb/kimberly/citace_upload/go/gpad2ace/2018_June_test/go_gpad_parser.pl
 
/home/acedb/kimberly/citace_upload/go/gpad2ace/2018_June_test/go_gpad_parser.pl
 
Line 130 - Will instead need a mapping between annotation relation and RO term id
 
Line 130 - Will instead need a mapping between annotation relation and RO term id
Line 45: Line 46:
  
 
Mappings (as of June 12th):
 
Mappings (as of June 12th):
colocalizes_with RO:0002325 110
+
*colocalizes_with RO:0002325 110
contributes_to RO:0002326 277
+
*contributes_to RO:0002326 277
enables RO:0002327 22903
+
*enables RO:0002327 22903
involved_in RO:0002331 32498
+
*involved_in RO:0002331 32498
part_of BFO:0000050 33772
+
*part_of BFO:0000050 33772
  
 
NOT annotations 224
 
NOT annotations 224
  
go_oa_parser modifications
+
= go_oa_parser modifications =
 
/home/postgres/work/citace_upload/go_curation/get_go_annotation_ace.pm
 
/home/postgres/work/citace_upload/go_curation/get_go_annotation_ace.pm
 
Line 56 - relations are stored in the gop_qualifier table
 
Line 56 - relations are stored in the gop_qualifier table
Line 59: Line 60:
  
 
Mappings (as of June 12th):
 
Mappings (as of June 12th):
colocalizes_with RO:0002325 0
+
*colocalizes_with RO:0002325 0
contributes_to RO:0002326 0
+
*contributes_to RO:0002326 0
enables RO:0002327 20
+
*enables RO:0002327 20
involved_in RO:0002331 334
+
*involved_in RO:0002331 334
part_of BFO:0000050 29
+
*part_of BFO:0000050 29
  
 
NOT annotations 0
 
NOT annotations 0

Revision as of 20:33, 27 June 2018

Parsing Scripts for ?RO_term Model and ?GO_annotation models

?RO_term

.ace parsing script (See /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl)

Output file: RO_terms.ace

File location: https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo

Right now, we will parse the obo file; the day may come, though, when we will want/need to parse the owl file.

Terms to Include: Include term where id namespace = BFO, RO, lower case text with no namespace: (e.g. results_in_acquisition_of_features_of)

Skip term where id namespace = CARO, CL, ENVO, GO, ObsoleteClass, PATO

Skip where is_obsolete: true

Fields to include, mapped to ?RO_term model tag (note that we can re-use much of the ?GO_term parsing script):

  • Id: -> RO_term
  • Name: -> Name
  • Status -> Valid
  • alt_id: -> Alt_id
  • Def: -> Definition (parse what is in quotes)
  • Synonym: -> Synonym (parse what is in caps to match Type and then the text that is in quotes
  • Data-version: -> Version

Review GO term parser for handling is_a relationships to populate Child, Parent, Index

Parsing report/sanity check: What terms have no ancestors? What terms have no descendants?

Update spelling of Descendant in ?GO_term model

go_gpad_parser modifications

/home/acedb/kimberly/citace_upload/go/gpad2ace/2018_June_test/go_gpad_parser.pl Line 130 - Will instead need a mapping between annotation relation and RO term id When just relation -> Annotation_relation When NOT|relation -> Annotation_relation_not This may be temporary as it was proposed at the NYC GO meeting to start using RO ids in place of text in the qualifier/relation column of at least the GPAD file Eventually this should also be the case for the Annotation extension relations, but there are some used in AEs that are not in RO

Mappings (as of June 12th):

  • colocalizes_with RO:0002325 110
  • contributes_to RO:0002326 277
  • enables RO:0002327 22903
  • involved_in RO:0002331 32498
  • part_of BFO:0000050 33772

NOT annotations 224

go_oa_parser modifications

/home/postgres/work/citace_upload/go_curation/get_go_annotation_ace.pm Line 56 - relations are stored in the gop_qualifier table Will need to output the same as above

Mappings (as of June 12th):

  • colocalizes_with RO:0002325 0
  • contributes_to RO:0002326 0
  • enables RO:0002327 20
  • involved_in RO:0002331 334
  • part_of BFO:0000050 29

NOT annotations 0