Evidence Code Ontology

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, 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

• Input file:
  • https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo

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