Difference between revisions of "Relations Ontology"
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Version UNIQUE Text | Version UNIQUE Text | ||
− | = Parsing | + | = Parsing Script for ?RO_term Model = |
*The parsing script to generate the ro_terms.ace file is on tazendra here: | *The parsing script to generate the ro_terms.ace file is on tazendra here: | ||
**/home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl | **/home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl |
Revision as of 15:52, 29 June 2018
Contents
Overview
- The Relations Ontology is used in WormBase to describe relations between entities in the database, e.g. genes and GO terms.
- The Relations Ontology was first incorporated into WormBase with the WS267 release.
?RO_term Model
?RO_term Name UNIQUE ?Text Status UNIQUE Valid Obsolete Alt_id ?Text Definition UNIQUE ?Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?Text Child Instance ?RO_term XREF Instance_of Parent Instance_of ?RO_term XREF Instance Attribute_of GO_annotation ?GO_annotation XREF Annotation_relation Not_GO_annotation ?GO_annotation XREF Annotation_relation_not Index Ancestor ?RO_term XREF Descendant Descendant ?RO_term XREF Ancestor Version UNIQUE Text
Parsing Script for ?RO_term Model
- The parsing script to generate the ro_terms.ace file is on tazendra here:
- /home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl
- Input file:
- Downloaded, manually processed version (see below) of https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo
- Output file:
- ro_terms.ace
- There are two types of entries in ro.obo
- Term
- Typedef
- At the moment, we include Term and Typedef entries according to the following criteria:
- 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
- Note that the terms we skip are used in the OWL representation of the Relations Ontology, but not in the OBO representation
- For the purposes of how the Relations Ontology will initially be used in WormBase, this should be fine
Update spelling to Descendant in ?GO_term model
- Update line 89 in (change e -> a)
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