Scope and Usage
ancillaryAminoAcidChangeType allows for the use of additional amino acid types which can be used to clarify and add depth to the primary-amino-acid-change-type. Additionally, this type allows a single annotation using a term not included in the primary list.
Additionally ancillaryAminoAcidChangeType can be used to annotate types experimentally discovered or derived with annotation tools such as VAT, SnpEff or ANNOVAR.
ancillaryAminoAcidChangeType List
Currently constraint to be a child of sequence_variant within the Sequence Ontology.
Examples:
ancillaryAminoAcidChangeType: (cardinality of 0..*)
- This attribute allows for a couple of possibilities.
1. First to allow additional detail in describing the location of the feature related to the variant. 2. Second, it allows the uses of terms that may better describe the feature of intrest, not offered in the primary list.
The first case:
| Type | Display Name | Code |
|---|---|---|
primaryAminoAcidChangeType |
frameshift_variant |
SO:0001589 |
ancillaryAminoAcidChangeType |
frameshift_elongation |
SO:0001909 |
| Type | Display Name | Code |
|---|---|---|
primaryAminoAcidChangeType |
missense_variant |
SO:0001580 |
ancillaryAminoAcidChangeType |
non_conservative_missense_variant |
SO:0001586 |
This method offers two levels of annotated detail. The primaryAminoAcidChangeType term enables higher-level grouping, and the ancillaryAminoAcidChangeType offers additional specifics on the nature of the variant.
The second case:
| Type | Display Name | Code |
|---|---|---|
ancillaryAminoAcidChangeType |
rare_amino_acid_variant |
SO:0002008 |
Annotation tools examples:
| Type | Display Name | Tool | Code |
|---|---|---|---|
ancillaryAminoAcidChangeType |
conserved_intergenic_variant |
SnpEff | SO:0002017 |
ancillaryAminoAcidChangeType |
stop_retained_variant |
VAT | SO:0001567 |
ancillaryAminoAcidChangeType |
upstream_gene_variant |
ANNOVAR | SO:0001631 |
Exclusions and Limitations
Additional terms can be submitted for review via the sequence ontology request a term