From 3ab9fbfbdc1cc75ebe2b022ca34a308b2366ff63 Mon Sep 17 00:00:00 2001 From: David Koslicki Date: Wed, 11 Sep 2024 21:25:45 +0100 Subject: [PATCH] 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 --- docs/architecture/ara/arax.md | 10 +++++----- docs/architecture/ars_usage.md | 2 +- docs/architecture/kp/rtx-kg2.md | 2 +- docs/architecture/workflows.md | 2 +- docs/development-guide/tutorials/workflows.md | 4 ++-- docs/faq.md | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/architecture/ara/arax.md b/docs/architecture/ara/arax.md index 8892b28f..2f183155 100644 --- a/docs/architecture/ara/arax.md +++ b/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 <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 <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 diff --git a/docs/architecture/ars_usage.md b/docs/architecture/ars_usage.md index 719b8d55..33b6b088 100644 --- a/docs/architecture/ars_usage.md +++ b/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 **``** 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 diff --git a/docs/architecture/kp/rtx-kg2.md b/docs/architecture/kp/rtx-kg2.md index 167aefb0..056c8c2c 100644 --- a/docs/architecture/kp/rtx-kg2.md +++ b/docs/architecture/kp/rtx-kg2.md @@ -70,7 +70,7 @@ cat <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 diff --git a/docs/architecture/workflows.md b/docs/architecture/workflows.md index e6918191..fdbe0b64 100644 --- a/docs/architecture/workflows.md +++ b/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 diff --git a/docs/development-guide/tutorials/workflows.md b/docs/development-guide/tutorials/workflows.md index c4908b13..e6e2a7ef 100644 --- a/docs/development-guide/tutorials/workflows.md +++ b/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 diff --git a/docs/faq.md b/docs/faq.md index c2ef916f..f45e0592 100644 --- a/docs/faq.md +++ b/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 and render the results. This is mainly helpful for debugging and development use. You can also enter a PK in the ID field .