Difference between revisions of "Relations Ontology"
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− | = Parsing Scripts for ?RO_term Model | + | = Parsing Scripts for ?RO_term Model = |
− | ?RO_term | + | ?RO_term class |
− | .ace parsing script | + | .ace parsing script for ?GO_term that can serve as a template |
(See /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl) | (See /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl) | ||
Line 8: | Line 8: | ||
RO_terms.ace | RO_terms.ace | ||
− | + | RO obo file location for download: | |
https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo | https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo | ||
Line 35: | Line 35: | ||
What terms have no descendants? | What terms have no descendants? | ||
− | =Update spelling | + | =Update spelling to Descendant in ?GO_term model = |
= go_gpad_parser modifications = | = 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 | ||
+ | |||
When just relation -> Annotation_relation | When just relation -> Annotation_relation | ||
− | When NOT|relation -> Annotation_relation_not | + | |
+ | 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 | 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 | Eventually this should also be the case for the Annotation extension relations, but there are some used in AEs that are not in RO | ||
Line 56: | Line 61: | ||
= 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 | ||
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Will need to output the same as above | Will need to output the same as above | ||
Revision as of 20:35, 27 June 2018
Contents
Parsing Scripts for ?RO_term Model
?RO_term class
.ace parsing script for ?GO_term that can serve as a template (See /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl)
Output file: RO_terms.ace
RO obo file location for download: 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 to 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