Evidence Code Ontology

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  • 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 Model

 ?ECO_term Name UNIQUE ?Text
          Status UNIQUE Valid
          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:
    • ?GO_annotation
    • ?Phenotype
    • ?Disease_model_annotation (will eventually replace ?GO_code with ?ECO_term)
  • Will remove ?GO_code in:
    • ?Cell

Additional model cleanup? Are these tags being used at all?

  1. ?Gene - remove ?GO_term tag and associated info?
  2. ?Sequence - remove ?GO_term tag and associated info?
  3. ?CDS - remove ?GO_term tag and associated info?
  4. ?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:
    • /home/acedb/kimberly/citace_upload/eco/ontology2ace/eco_obo_to_eco_ace.pl
  • Output file:
    • eco_terms.ace
  • There are two types of entries in ro.obo
    • Term
    • Typedef
  • 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
5 Reference Leave PMID or DOI as is; add corresponding WB:WBPaper id; identifiers are pipe-separated PMID:10978280|WB:WBPaper00004310
6 Evidence Leave as is ECO:0000314
7 With/From Check UniProtKB: entries for possible conversion to WB:WBGene; otherwise leave entry as is WB:WBGene00000001
8 Interacting taxon Leave as is NCBITaxon:273526
9 Annotation date Leave as is 2006-02-03T12:26
10 Assigned_by Leave as it WB
11 Annotation extensions If relation is a text string, convert to an id according RO mapping table. Otherwise, leave as is. RO:0002233(WB:WBGene00000584)
12 Annotation properties Most will stay as is, except for history (see below). contributor-id=https://orcid.org/0000-0002-1706-4196%7Ccomment=action:Updated by Kimberly Van Auken|model-state=deleted

  • Notes:
    • For names, may need to escape forward slashes
    • There are 40 obsolete ECO terms in the releases/2020-05-15

  • Running the script:
  1. 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
  2. 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
  • 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