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 |