Evidence Code Ontology

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Overview

  • 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
                        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:
    • ?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
Definition def: Add 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
Child n/a n/a n/a
Parent is_a: Add is_a parent id as is ECO:0000015
Version data-version: Add text following 'data-version:' releases/2020-05-15


  • Notes and Questions:
    • For names, may need to escape forward slashes
    • There are 40 obsolete ECO terms in the releases/2020-05-15
    • Include bracketed evidence on definitions? We aren't doing this for GO, but we probably should. Would we need to extend the end quotation until after the references?

Example obo and ace entries

obo entry for IMP

  • [Term]
  • id: ECO:0000315
  • name: mutant phenotype evidence used in manual assertion
  • def: "A type of mutant phenotype evidence that is used in a manual assertion." [ECO:MCC]
  • subset: valid_with_chemical_entity
  • subset: valid_with_gene
  • subset: valid_with_protein
  • subset: valid_with_protein_complex
  • synonym: "IMP" EXACT [GOECO:IMP]
  • synonym: "inferred from mutant phenotype" EXACT [GOECO:IMP]
  • xref: GOECO:IMP "inferred from mutant phenotype"
  • is_a: ECO:0000015 ! mutant phenotype evidence
  • is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion
  • intersection_of: ECO:0000015 ! mutant phenotype evidence
  • intersection_of: used_in ECO:0000218 ! manual assertion
  • property_value: seeAlso http://geneontology.org/page/imp-inferred-mutant-phenotype xsd:string
  • created_by: mchibucos
  • creation_date: 2011-10-28T05:12:49Z

ace entry for IMP

  • ECO_term : "ECO:0000315"
  • Name "mutant phenotype evidence used in manual assertion"
  • Status "Valid"
  • Definition "A type of mutant phenotype evidence that is used in a manual assertion."
  • Synonym Exact "IMP"
  • Synonym Exact "inferred from mutant phenotype"
  • Parent "ECO:0000015"
  • Parent "ECO:0007634"
  • Version "Relations Ontology releases/2020-02-26"

Changes to ?GO_annotation parsing scripts

Protein2GO GPAD

  • Latest parsing script: /home/acedb/kimberly/citace_upload/go/gpad2ace/2020_July
  • Keep populating GO_code tag (lines 159 and 160)
  • Add populating ECO_term tag
    • ECO_term is in $evicode (Column 7) in GPAD input file
    • Populate value in .ace file as is, e.g. ECO:0000315
      • ECO_term "ECO:0000315"

Noctua GPAD

  • Latest parsing script: /home/acedb/kimberly/citace_upload/go/gocam2ace/2020_July
  • Keep populating GO_code tag (lines 153 and 154)
  • Add populating ECO_term tag
    • ECO_term is in $evicode (Column 7) in GPAD input file
    • Populate value in .ace file as is, e.g. ECO:0000315
      • ECO_term "ECO:0000315"

OA Annotations

  • Latest parsing script: /home/postgres/work/citace_upload/go_curation
  • Keep populating GO_code tag (line 83)
  • Add populating ECO_term tag
    • Use value in goinference
    • Map to ECO term (there is a mapping in /home/acedb/kimberly/citace_upload/go/gocam2ace/2020_July in lines 304-328)
    • Populate value in .ace file from mapping, e.g. ECO:0000315
      • ECO_term "ECO:0000315"
    • List of mappings to use (from gocam2ace parsing script):
      • $ecoToGoCode{"ECO:0000250"} = "ISS";
      • $ecoToGoCode{"ECO:0000270"} = "IEP";
      • $ecoToGoCode{"ECO:0000304"} = "TAS";
      • $ecoToGoCode{"ECO:0000303"} = "NAS";
      • $ecoToGoCode{"ECO:0000307"} = "ND";
      • $ecoToGoCode{"ECO:0000305"} = "IC";
      • $ecoToGoCode{"ECO:0000314"} = "IDA";
      • $ecoToGoCode{"ECO:0000315"} = "IMP";
      • $ecoToGoCode{"ECO:0000316"} = "IGI";
      • $ecoToGoCode{"ECO:0000353"} = "IPI";
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