Evidence Code Ontology
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Revision as of 14:56, 1 June 2020 by Vanaukenk (talk | contribs) (→ECO obo file to WB ace file mappings)
Contents
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?
- ?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:
- /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 test 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
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"
Status "Valid" Definition "A type of mutant phenotype evidence that is used in a manual assertion." [ECO:MCC] Name "developmentally replaces" Version "Relations Ontology releases/2020-02-26"