Table 1.
Bioeditor data model: (A) Basic triplet statement; (B) Relations; (C) Evidence
| 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 |
CV Controlled vocabulary, HGVS Human Genome Variation Society, ChEBI Chemical Entities of Biological Interest, GO Gene Ontology, ECO Evidence and Conclusion Ontology