Update classifications-and-ontologies.md

Line breaks for table and tabs for SNV tree
progenetix · Dec 7, 2023 · efb9e03 · efb9e03
1 parent 2337bdd
commit efb9e03
Showing 1 changed file with 34 additions and 8 deletions.
diff --git a/docs/classifications-and-ontologies.md b/docs/classifications-and-ontologies.md
@@ -144,17 +144,43 @@ This table is maintained in parallel with the [Beacon v2 documentation](http://d
 
 | [EFO](http://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO       | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#copynumberchange)[^1] | Notes |
 | ------------------------------------------- | ------------------------------------------------------------------------------ | -------------------------------------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | ----- |
-| <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) gain  | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
-| [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain   | <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> low-level gain |                                                                                                                             |
-| [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region                                             |
-| [`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification  | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain[^4]  | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
-| [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) copy number loss            | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> loss            | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence              |
-| [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss  | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> low-level loss  |                                                                                             |
-| [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss  | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> 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<br/><nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss   | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region)                                          |
+| <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr><br/> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) <br/> copy_number_gain | <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> gain  | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
+| <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr><br/> low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) <br/> copy_number_gain | <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr><br/>low-level gain | |
+| <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr><br/> high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) <br/> copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr><br/> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
+| <nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr><br/> focal genome amplification  | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) <br/> copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr><br/> high-level gain[^4]  | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
+| <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr><br/> copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) <br/> copy_number_loss | <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr><br/> loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
+| <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss  | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) <br/> copy_number_loss | <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr><br/> low-level loss  | |
+| <nobr>[`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073)</nobr><br/> high-level copy number loss  | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) <br/> copy_number_loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr><br/> high-level loss  | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
+| <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr><br/> complete genomic deletion   | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) <br/> copy_number_loss | <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss   | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |
 
 -------------------------------------------------------------------------------
+
 ## Sequence Variation (SNV Ontology)
+
+=== "Used terms"
+
+```
+id: SO:0001059
+label: sequence_alteration
+  |
+  |-id: SO:0000159
+  | label: deletion
+  |
+  |-id: SO:0000667
+  | label: insertion
+  |
+  |-id: SO:1000002
+  | label: substitution
+      |
+      |-id: SO:0002007
+      | label: MNV (multiple nucleotide variant)
+      |
+      |-id: SO:0001483
+        label: SNV (single nucleotide variant)
+```
+
+=== "Extended tree"
+
 ```
 id: SO:0001059
 label: sequence_alteration