Evidence Code Ontology
From WormBaseWikiJump to navigationJump to search
- 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
- 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