Little fixes (#82)

* Typo fix

* add link to UI

* link the other workflow doc

* fix link

* correct ARAX link

* fix ARAX link

* more link fixing

* one more URL fix

* another link fix

---------

Co-authored-by: Richard Bruskiewich <[email protected]>

docs/architecture/ara/arax.md

@@ -7,9 +7,9 @@
 * Integrated with numerous Knowledge Sources and Knowledge Providers, with automatic (or optionally, manual) specification of what sources and providers are utilized. 
 
 ## Technical User Guide to ARAX
-There are two main modes for interacting with ARAX: the first is via posting TRAPI messages to the ARAX [API](https://arax.ncats.io/api/arax/v1.0/ui/). Examples of doing this are included [here](https://github.com/RTXteam/RTX/tree/master/code/ARAX/Examples).
+There are two main modes for interacting with ARAX: the first is via posting TRAPI messages to the ARAX [API](https://arax.transltr.io/api/arax/v1.4/ui/). Examples of doing this are included [here](https://github.com/RTXteam/RTX/tree/master/code/ARAX/Examples).
 
-The second way to interact with ARAX is via the [GUI](https://arax.ncats.io/). There, you will see four different query types:
+The second way to interact with ARAX is via the [GUI](https://arax.transltr.io/). There, you will see four different query types:
 1. You can build a query graph by clicking on this icon: ![](https://www.dropbox.com/s/uhe2qtqyzei1aw7/graph.PNG?raw=1)
 2. You can paste in a `query_graph` element in a JSON TRAPI message (circumventing the need to manually POST TRAPI queries) by clicking on this icon: ![](https://www.dropbox.com/s/3gw48t4fp5ty33s/JSON.PNG?raw=1)
 3. You can enter ARAXi domain specific language commands by clicking on this icon: ![](https://www.dropbox.com/s/khh6whk095vg63c/DSL.PNG?raw=1)
@@ -65,7 +65,7 @@ cat <<EOF >onehop.json
 EOF
 
 curl -X POST \
-     "https://arax.ncats.io/api/arax/v1.4/query?bypass_cache=false" \
+     "https://arax.transltr.io/api/arax/v1.4/query?bypass_cache=false" \
      -H  "accept: application/json" \
      -H  "Content-Type: application/json" \
      -d @onehop.json
@@ -76,7 +76,7 @@ should result in something similar to this response:
   "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld",
   "datetime": "2021-05-10 11:56:19",
   "description": "Normal completion",
-  "id": "https://arax.ncats.io/api/arax/v1.1/response/9182",
+  "id": "https://arax.transltr.io/api/arax/v1.4/response/9182",
   "logs": [
     {
       "code": "",
@@ -234,7 +234,7 @@ cat <<EOF >kitchensink.json
 EOF
 
 curl -X POST \
-     "https://arax.ncats.io/api/arax/v1.1/query?bypass_cache=false" \
+     "https://https://arax.transltr.io/api/arax/v1.4/query?bypass_cache=false" \
      -H  "accept: application/json" \
      -H  "Content-Type: application/json" \
      -d @kitchensink.json

docs/architecture/ars_usage.md

@@ -62,7 +62,7 @@ Results of the query can be found in the ARS messages: https://ars-prod.transltr
 
 The ARAX web interface can also be used to consult the result of your query: 
 
-1. Go to https://arax.ncats.io
+1. Go to [https://arax.transltr.io/](https://arax.transltr.io/)
 2. Go to the **`<id>`** tab (in **Query**)
 3. Copy the run ID previously obtained in the text box
 4. Click on **`Load`** to see the detailed results of your query

docs/architecture/kp/rtx-kg2.md

@@ -70,7 +70,7 @@ cat <<EOF >onehop.json
 EOF
 
 curl -X POST \
-     "https://arax.ncats.io/api/rtxkg2/v1.3/query?bypass_cache=false" \
+     "https://kg2.transltr.io/api/rtxkg2/v1.4/query?bypass_cache=false" \
      -H  "accept: application/json" \
      -H  "Content-Type: application/json" \
      -d @onehop.json

docs/architecture/workflows.md

@@ -90,7 +90,7 @@ In this fashion, a user can precisely specify what sort of workflow they desire.
 Each Translator component is expected to implement a set of operations that it can perform. This is done via 
 the OpenAPI specification utilizing the `x-trapi` extension. Directions on how to implement this can be found
 [here](https://github.com/NCATSTranslator/OperationsAndWorkflows/wiki/How-to-%22do%22-operations#advertising-operations),
- with a real-world example [here](https://arax.ncats.io/test/api/arax/v1.2/openapi.json).
+ with a real-world example [here](https://arax.transltr.io/api/arax/v1.4/openapi.json).
 
 # Implementing operations
 Please see the [Guide for developers](../development-guide/tutorials/workflows.md) for developer details about how 

docs/development-guide/tutorials/workflows.md

@@ -4,7 +4,7 @@ The Operations and Workflow effort aims to define and standardize how Translator
 
 The goal is to create standardized operations, build reference implementations, and develop workflows that can be composed and run within the Translator ecosystem. The result is a (continually growing) set of formal definitions, tools, and language that enable developers to discover, interpret, and control Translator operations with greater clarity. 
 
-The [Workflow Runner](https://github.com/NCATSTranslator/workflow-runner) handles the identification of which service can respond to which operation, send to the appropriate endpoints, combine responses, and repeat for all operations. Some ARAs can also handle Workflow operations. 
+The [Workflow Runner](https://github.com/NCATSTranslator/workflow-runner) handles the identification of which service can respond to which operation, send to the appropriate endpoints, combine responses, and repeat for all operations. Some ARAs can also handle Workflow operations. Please see [here](../../architecture/workflows.md) for more information about the workflow runner.
 
 The [Curated Query Service (CQS)](https://github.com/TranslatorSRI/CQS/tree/main) is an example of a service that leverages the Operations & Workflows. 
 
@@ -150,7 +150,7 @@ Once the workflow is saved, use the following cURL command to send the request t
 
 ```bash
 curl -X POST \
-     "https://arax.ncats.io/api/arax/v1.4/query?bypass_cache=false" \
+     "https://arax.transltr.io/api/arax/v1.4/query?bypass_cache=false" \
      -H  "accept: application/json" \
      -H  "Content-Type: application/json" \
      -d @workflow.json

docs/faq.md

@@ -16,8 +16,8 @@ Here are two ways to convert from natural language to a CURIE:
 1. The [SRI Name Resolver](https://name-resolution-sri.renci.org/docs), specifically the `/lookup` endpoint, can take natural language and find a CURIE associated with it.
 2. The [ARAX UI](https://arax.transltr.io/) has a `Synonyms` feature on the left bar under the heading `Tools`. In it, you can type a term (with autocomplete) and find equivalent CURIES. This approach uses both the SRI Name Resolver and additional information derived from RTX-KG2.
 
-### How do I compute the Normalized Google Distance (NGD) between two concepts?
-The endpoint [https://arax.transltr.io/api/arax/v1.4/ui/#/PubmedMeshNgd/pubmed_mesh_ngd](https://araxtransltr.io/api/arax/v1.4/ui/#/PubmedMeshNgd/pubmed_mesh_ngd) takes two natural language inputs (terms occurring in UMLS) and returns the NGD between them.
+### How do I compute the Normalized Google Distance (NGD) between two concepts
+The endpoint [https://arax.transltr.io/api/arax/v1.4/ui/#/PubmedMeshNgd/pubmed_mesh_ngd](https://arax.transltr.io/api/arax/v1.4/ui/#/PubmedMeshNgd/pubmed_mesh_ngd) takes two natural language inputs (terms occurring in UMLS) and returns the NGD between them.
 
 ### How can I quickly view a TRAPI response?
 The ARAX UI [https://arax.transltr.io/](https://arax.transltr.io/) can take a TRAPI response <img src="https://github.com/user-attachments/assets/780025a6-9907-4802-87ba-238896c002a5" width="150"> and render the results. This is mainly helpful for debugging and development use. You can also enter a PK in the ID field <img src="https://github.com/user-attachments/assets/c3cdda80-9790-4324-99a8-057bb9a84202" width="150">.