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progenetix · Feb 1, 2024 · 8cf2241 · 8cf2241
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diff --git a/docs/beaconplus.md b/docs/beaconplus.md
@@ -80,7 +80,7 @@ collections of MongoDB databases. These collections are addressed by scoped quer
 Filters represent a way to allow the resource provider to direct "self-scoped" query values to the corresponding attributes in their backend resource. In the Progenetix implementation, a lookup table followed by scope assignment is used to map prefixed filter values to the correct  attributes and collections. Most of the filter options are
 based on ontology terms or identifiers in CURIE format (e.g. `NCIT:C4033`, `cellosaurus:CVCL_0030` or `PMID:16004614`). For use case examples please
 look below; documentation of available ontologies and how to find out about available
-terms can be found on the [Classifications and Ontologies](classifications-and-ontologies.md) page.
+terms can be found on the [Classifications and Ontologies](common/classifications-and-ontologies.md) page.
 
 In Beacon v2, the new `FilteringTerms` schema adds options to specify different
 types of filters (`OntologyFilter`, `AlphanumericFilter`, `CustomFilter`) which can

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -38,7 +38,7 @@ terms used in a query. More information is available in the [Filtering Terms](be
 
 ## 2022-01-17: Introducing `variant_state` classes for CNVs
 
-More information can be found in the [description of ontology use for CNVs](classifications-and-ontologies.md#genomic-variations-cnv-ontology).
+More information can be found in the [description of ontology use for CNVs](common/classifications-and-ontologies.md#genomic-variations-cnv-ontology).
 
 ## 2022-01-10: BUG FIX Frequency Maps
 

diff --git a/docs/classifications-and-ontologies.md → .../common/classifications-and-ontologies.md b/docs/classifications-and-ontologies.md → .../common/classifications-and-ontologies.md
diff --git a/docs/common/plotting.md b/docs/common/plotting.md
@@ -10,7 +10,6 @@ The standard format for (plot-)images generated on Progenetix is Scalable Vector
 
 On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.
 
-
 ## The `byconaut` plotting library
 
 Functionality of the Progenetix and cancercellline.org plotting API is provided

diff --git a/docs/javascripts/tablesort.js b/docs/javascripts/tablesort.js
diff --git a/docs/news/2022-01-17-cnv-state-classes.md b/docs/news/2022-01-17-cnv-state-classes.md
@@ -5,4 +5,4 @@ description: More granular annotation of CNV types
 date: 2022-01-17
 ---
 
-More information can be found in the [description of ontology use for CNVs](classifications-and-ontologies.md#genomic-variations-cnv-ontology).
+More information can be found in the [description of ontology use for CNVs](common/classifications-and-ontologies.md#genomic-variations-cnv-ontology).
diff --git a/docs/pgxRpi.md b/docs/pgxRpi.md
@@ -4,7 +4,7 @@
 
 ## Retrieve biosample information 
 
-You can select biosamples from specific groups of interests, chosen by a filter. The description about _filters_ is [here](https://docs.progenetix.org/classifications-and-ontologies/).
+You can select biosamples from specific groups of interests, chosen by a filter. The description about _filters_ is [here](https://docs.progenetix.org/common/classifications-and-ontologies/).
 
 ```
 biosamples <- pgxLoader(type="biosample", filters = "NCIT:C3512",codematches = TRUE)

diff --git a/mkdocs.yaml b/mkdocs.yaml
@@ -7,7 +7,7 @@ repo_url: https://github.com/progenetix/progenetix-web
 
 # vars for common files (shared between sites) #################################
 
-api_site_label: progenetix.org
+api_site_label: '[Progenetix](https://progenetix.org)'
 api_web_root: https://progenetix.org
 
 ################################################################################
@@ -22,7 +22,7 @@ nav:
   - Analysis in R - pgxRpi: pgxRpi
   - Plotting & Visualizations: common/plotting
   - Use Case Examples: use-cases
-  - Classifications, Ontologies & Standards: classifications-and-ontologies
+  - Classifications, Ontologies & Standards: common/classifications-and-ontologies
   - Publication Collection: publication-collection
   - Data Review: progenetix-data-review
   - Technical Notes: technical-notes
@@ -105,6 +105,6 @@ extra:
       link: https://github.com/progenetix
 extra_css:
   - css/theme_overrides.css
-extra_javascript:
-  - https://cdnjs.cloudflare.com/ajax/libs/tablesort/5.2.1/tablesort.min.js
+# extra_javascript:
+#   - https://cdnjs.cloudflare.com/ajax/libs/tablesort/5.2.1/tablesort.min.js
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,7 +10,6 @@ The standard format for (plot-)images generated on Progenetix is Scalable Vector

		On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.


		## The `byconaut` plotting library

		Functionality of the Progenetix and cancercellline.org plotting API is provided
Expand Down