Evidence Code Ontology
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- 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, and is proposed to eventually fully replace ?GO_code.
?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 ?ECO_term XREF Parent Parent ?ECO_term XREF Child Version UNIQUE Text
Other models affected for WS278
- Will replace ?GO_code with ?ECO_term in:
- ?Disease_model_annotation (will eventually replace ?GO_code with ?ECO_term)
- Will remove ?GO_code in:
- ?Gene - remove ?GO_term tag and associated info?
- ?Sequence - remove ?GO_term tag and associated info?
- ?CDS - remove ?GO_term tag and associated info?
- ?Transcript - remove ?GO_term tag and associated info?
Parsing Script for ?ECO_term Model
- The parsing script to generate the eco_terms.ace file is on tazendra here:
- Output file:
- There are two types of entries in ro.obo
- We'll only include the Term entries
ECO obo file to WB ace file mappings
|ace field||ECO field||Action||Example|
|ECO_term||id:||Add ECO id as is||ECO:0000052|
|Name||name:||Add name as is (but see below)||suppressor/enhancer interaction phenotypic evidence|
|Status||is_obsolete:||Populate with 'Valid' unless 'is_obsolete: true', then populate with Obsolete*||Valid|
|Alt_id||alt_id:||Add alt_id as is||ECO:0005018|
|Definition||def:||Remove quotation marks; add remaining text as is||A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. [ERO:0001362, url:http\://www.ncbi.nlm.nih.gov/books/NBK21589/\,http\://cores.ucsf.edu/protein-assay.html]|
|Synonym||synonym||Remove quotation marks; populate type from bracketed text; add remaining text as is||Exact gain-of-function mutant phenotype evidence|
|Parent||is_a:||Add is_a parent id as is||ECO:0000015|
|Version||data-version:||Add text following 'data-version:'|
- For names, may need to escape forward slashes
- There are 40 obsolete ECO terms in the releases/2020-05-15
- 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