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Table 1 Bioeditor data model: (A) Basic triplet statement; (B) Relations; (C) Evidence

From: A new bioinformatics tool to help assess the significance of BRCA1 variants

Element CV/ontology Example
A. Annotation
 Subject HGVS nomenclature BRCA1-p.Cys61Gly
 Relation cv_modification_effect.obo decreases
 Object Protein BARD1 [neXtProt:NX_Q99728]
ChEBI Zn2+ [CHEBI:29105]
GO ubiquitin-protein transferase activity [GO:0004842]
Protein property protein abundance [PP:0001]
Mammalian phenotype premature death [MP:0002083]
B. Relations
 No impact No significant effect observed compared to wild-type
  • Does not cause phenotype No observable morphological, physiological and behavioral characteristics in the mutant compared to the wild-type
 Impacts Some significant effect observed compared to wild-type
  • Causes phenotype Some observable morphological, physiological and behavioral characteristics in the mutant compared to the wild-type
  • Increases Some significant increase observed in a quantifiable measure compared to wild-type
  • Decreases Some significant decrease observed in a quantifiable measure compared to wild-type
  • Gains function Mutant protein acquires a property absent from the wild-type (new substrate, new cellular localization, etc.)
C. Evidence
 Evidence code(s) ECO Immunoprecipitation evidence used in manual assertion [ECO:0005644]
 Protein origin NCBI taxonomy Homo sapiens [NCBITaxID:9606]
 Biological model species, cell type, anatomy, cell line NCBI taxonomy HEK293T [CVCL_0063]
CALOHA anatomy ontology
Cellosaurus
 Phenotype intensity Mild/moderate/severe Severe
 Evidence quality Gold/Silver Gold
 Reference Cross-reference to PubMed PUBMED:20103620
  1. CV Controlled vocabulary, HGVS Human Genome Variation Society, ChEBI Chemical Entities of Biological Interest, GO Gene Ontology, ECO Evidence and Conclusion Ontology