more docs

docs/API.md

@@ -1,5 +1,19 @@
 # API Documentation
 
+## Beacon Endpoints
+
+==TBD==
+
+## Service Endpoints
+
+Additionally to the standard Beacon endpoints provided for the Beacon framework and default data model
+`bycon` also has a number of service endpoints. Some of them are used to provide direct Beacon support (e.g. `/endpoints` or `/schemas` to implement endpoints accessed from Beacon responses), while others
+provide more specialized functionality (e.g. `/cytomapper`).
+
+More information:
+
+* [list of bycon services](/generated/services)
+
 ## Parameters  [... more](/generated/argument_definitions)
 
 The `bycon` package supports number of parameters for filtering and querying the data which includes and extends
@@ -9,20 +23,17 @@ invoked through HTTP requests and as command line arguments.
 Only parameters sefined in `config/argument_definitions.yaml` will be
 interpreted. Those parameters are listed in [this document](/generated/argument_definitions).
 
-## Beacon Endpoints
-
-==TBD==
-
-## Service Endpoints [... more](/generated/services)
-
-==TBD==
-
 ## Endpoint Tests [... more](/tests)
 
 ==TBD==
 
-## Plotting [... more](/plotting)
+## Plotting
 
 The `byconServices` package inside `bycon` provides a number of plotting functions which can be used to visualize the data in the database. Generally
 plot functionality is focussed on generating CNV visualizations for per-sample and
-aggregated (e.g. frequencyplots). Detailed information with use cases as well as plot parameter documentation can be found on [this page](/plotting).
+aggregated CNV data (e.g. frequencyplots). Additionally some geographic map projectins are provided e.g. for samples and metadata.
+
+More information can be found on these pages:
+
+* plot documentation on [this page](/plotting)
+* plot [parameters and defaults](/generated/plot_defaults)

docs/generated/services.md

@@ -120,7 +120,15 @@ matching gene IDs.
 
 ## `/geolocations`
 
-None
+==TBD==
+
+#### Examples
+
+* <https://progenetix.org/services/geolocations?city=zurich>
+* <https://progenetix.org/services/geolocations?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000>
+* <https://progenetix.org/services/geolocations?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000&output=map>
+* <http://progenetix.org/services/geolocations?inputfile=https://raw.githubusercontent.com/progenetix/pgxMaps/main/rsrc/locationtest.tsv&debug=&output=map&>
+* <http://progenetix.org/cgi/bycon/services/geolocations.py?city=New&ISO3166alpha2=UK&output=map&markerType=marker>
 
 
 ## `/ids`
@@ -145,7 +153,9 @@ None
 
 ## `/ontologymaps`
 
-None
+#### Examples
+
+* <https://progenetix.org/services/ontologymaps/?filters=NCIT:C3222>
 
 
 ## `/pgxsegvariants`
@@ -155,7 +165,17 @@ None
 
 ## `/publications`
 
-==TBD==
+The _publications_ servive provides API functionality for accessing the
+Progenetix [publications](http://progenetix.org/publications/) collection, which
+represents curated information about several thousand articles reporting
+genome-wide screening experiments in cancer. 
+
+#### Examples
+
+* <https://progenetix.org/services/publications/?filters=PMID>
+* <http://progenetix.org/services/publications/?filters=PMID,genomes:&gt;200,arraymap:&gt;1>
+* <http://progenetix.org/services/publications/?filters=PMID:22824167&method=details>
+* <http://progenetix.org/services/publications/?geoLongitude=8.55&geoLatitude=47.37&geoDistance=100000>
 
 
 ## `/samplemap`