Evidence Code Ontology
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Overview
- The Evidence and Conclusion Ontology is used in WormBase to record evidence used for assertions in curation data models.
- The Evidence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278.
?ECO_term Model
?ECO_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 ?ECO_term XREF Instance_of Parent Instance_of ?ECO_term XREF Instance Attribute_of GO_annotation ?GO_annotation XREF ?ECO_code Index Ancestor ?ECO_term XREF Descendant Descendant ?ECO_term XREF Ancestor Version UNIQUE Text
Parsing Script for ?ECO_term Model
TO BE ADDEDinformation below is wrt RO parsing
- 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 filtering step should be fine
- Running the script:
- In the /home/acedb/kimberly/citace_upload/ro/ontology2ace directory on tazendra, use the wget command and the above URL to download the ro.obo input file
- Greek characters used in some of the definitions for the RO terms (as an example, see id: BFO:0000063 name: precedes) need to be converted to text that ACeDB can render by doing the following (note that we tried to incorporate this as part of the script, but couldn't figure out a way to correctly recognize these characters programtically):
- In one terminal window, open the ro.obo file in a text editor
- In a second terminal window, open the convertGreekVim file in a text editor
- Globally replace the lower case alpha and omega symbols in ro.obo by copying and pasting the appropriate global replacement commands from convertGreekVim, e.g. :%s/α/alpha/g
- Sanity check:
- 26 substitutions of lower-case alpha on 10 lines
- 24 substitutions of lower-case omega on 9 lines
- Sanity check:
- Once the Greek characters have been replaced, run the parsing script and change the name of the output file from ro_terms.ace to ro_terms_WSnnn.ace