From 2337bdd0b227b0ea429576f6333d19fd413e75b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kay=20von=20Gr=C3=BCnigen?= Date: Thu, 7 Dec 2023 11:32:29 +0100 Subject: [PATCH] Update classifications-and-ontologies.md --- docs/classifications-and-ontologies.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/classifications-and-ontologies.md b/docs/classifications-and-ontologies.md index 4852e3a2..da0c56b4 100644 --- a/docs/classifications-and-ontologies.md +++ b/docs/classifications-and-ontologies.md @@ -152,6 +152,7 @@ This table is maintained in parallel with the [Beacon v2 documentation](http://d | [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or
[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level loss | | | [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or
[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted | | [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or
[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) | + ------------------------------------------------------------------------------- ## Sequence Variation (SNV Ontology) ``` @@ -221,6 +222,7 @@ label: sequence_alteration |-id: SO:0001483 label: SNV (single nucleotide variant) ``` + | [Sequence Ontology](http://www.sequenceontology.org/) | Definition | | ------------------------------------------- | --------------------------------------------- | | [`SO:0001059`](http://www.sequenceontology.org/browser/current_release/term/SO:0001059) sequence_alteration | A sequence alteration is a sequence feature whose extent is the deviation from another sequence. |