Karafecho patch 2 (#100)

* Deleted outdated table and text. Added a sentence on the UI and Jupyter notebook access points. * Update faq.md * Added a new section to provide an overview of Translator functionalities, access methods, and applications. * Updated description of query types. * Update faq.md * Update consortium_development_guidelines.md * Update ui.md * Update ci.md * Update deployment.md * Figure 3 should probably be replaced with a UI screenshot. As a shortcut, I revised the text to indicate that the screenshot is from an experimental UI. * Removed individual ARA pages in favor of Wiki pages. * Removed individual pages in favor of Wiki pages. * Update license.md * Added disclaimer re licensing. * Update index.md
NCATSTranslator · Oct 3, 2024 · 95d10cb · 95d10cb
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diff --git a/docs/architecture/ara/index.md b/docs/architecture/ara/index.md
@@ -8,13 +8,13 @@ Translator "Autonomous Relay Agents" (ARAs) build build upon the knowledge contr
 
 - [Autonomous Relay Agent usage tutorials](../../development-guide/tutorials/index.md)
 
-## Existing Translator ARA's
+## Existing Translator ARAs
 
 | Team                                                                                  | Name                                                               | Documentation                                                                                                | Github Repository                                                               |
 | ------------------------------------------------------------------------------------- | ------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------- |
 | [Ranking Agent](../../teams/ranking-agent.md) | Aragorn                                          | [Aragorn Page](aragorn.md)                               | [ranking-agent/aragorn](https://github.com/ranking-agent/aragorn)               |
-| [Expander Agent](../../teams/expander-agent.md)                                       | ARAX                                                               | [ARAX Page](arax.md)<br/>[ARAX Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/ARAX)            | [RTXteam/RTX](https://github.com/RTXteam/RTX)                                   |
+| [Expander Agent](../../teams/expander-agent.md)                                       | ARAX                                                               | [ARAX Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/ARAX)            | [RTXteam/RTX](https://github.com/RTXteam/RTX)                                   |
 | (im)Proving Agent                                                                     | Scalable Precision Medicine<br>Oriented Knowledge Engine ('SPOKE') | [SPOKE Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/imProving-Agent)                         | [BaranziniLab/PSEV](https://github.com/BaranziniLab/PSEV)                       |
-| [Exploring Agent](../../teams/exploring-agent.md)                                                                        | [BioThings Explorer](https://explorer.biothings.io/)               | [BioThings Explorer Page](bte.md) [BioThings Explorer Wiki](<https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-Explorer-(BTE)>) | [biothings/biothings_explorer](https://github.com/biothings/biothings_explorer) |
+| [Exploring Agent](../../teams/exploring-agent.md)                                                                        | [BioThings Explorer](https://explorer.biothings.io/)               | [BioThings Explorer Wiki](<https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-Explorer-(BTE)>) | [biothings/biothings_explorer](https://github.com/biothings/biothings_explorer) |
 | Explanatory Agent                                                                     | xARA                                                               | [xARA Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Explanatory-Agent)                        |                                                                                 |
 | Unsecret Agent                                                                        | Unsecret Agent                                                     | [Unsecret Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/UnSecret-Agent)                       | [webyrd/mediKanren](https://github.com/webyrd/mediKanren)                       |
diff --git a/docs/architecture/index.md b/docs/architecture/index.md
@@ -5,8 +5,7 @@ The Translator platform consists of five main components, shown in the diagram b
 information abstracted from one or more underlying ‘knowledge sources’. Autonomous Relay Agents (ARAs) build upon the 
 knowledge contributed by KPs by way of reasoning and inference across KPs. The Autonomous Relay System (ARS) functions
 as a central relay station and broadcasts user queries to the broader Translator
-ecosystem and, in turn, compiles results. A user interface (UI) is under development and intended to serve as a public UI to the Translator system.
-Finally, a Standards and Reference Implementation (SRI) Component provides services and community-based collaboration
+ecosystem and, in turn, compiles results. A [Translator UI](https://ui.transltr.io/) is under development and intended to serve as the public interface to the Translator system. Finally, a Standards and Reference Implementation (SRI) Component, while not directly contributing to the Translator architecture, provides services and community-based collaboration
 guidance related to the development, adoption, and implementation of the standards needed to achieve the overall
 implementation goals of the Translator system.
 
@@ -34,7 +33,7 @@ ibuprofen. Translator also provided answers that are correct but not terribly in
 user intent such as caffeine (an adjuvant included in certain pain medication). Also included among Translator answers
 to the example query are answers such as naltrexone, an opioid antagonist, which may not be expected by users. In support of naltrexone, Translator
 provided evidence and provenance indicating that naltrexone indeed may be used to treat chronic pain, as highlighted
-below. Translator evidence and provenance included ranked answers with scores, primary and secondary knowledge sources
+below in a screenshot from an experimental UI. Translator evidence and provenance included ranked answers with scores, primary and secondary knowledge sources
 behind any assertions, PubMedCentral or PubMed identifiers, and links to abstracts, etc. 
 
 This sort of serendipitous discovery, or unexpected insight, represents the type of scientific discovery that
@@ -51,4 +50,4 @@ In terms of impact, Translator is currently being used to promote serendipitous
 in a variety of disease spaces, including Fanconi anemia, systemic sclerosis, cystic fibrosis, Parkinson’s disease, 
 and drug-induced liver injury.
 
-Further technical details about the components of the Translator architecture are provided within the [**Development Guide**](../development-guide/index.md).
+Further technical details about the components of the Translator architecture are provided within the [**Development Guide**](../development-guide/index.md).
diff --git a/docs/architecture/kp/index.md b/docs/architecture/kp/index.md
@@ -13,17 +13,17 @@ Knowledge Providers (KPs) contribute domain-specific, high-value information abs
 | Team                    | Name                                | Documentation                                                                                                                        | Github Repository                                                                                               |
 | ----------------------- | ----------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
 | Molecular Data Provider | Molecular Data Provider ('MolePro') | [Molecular Data Provider Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Molecular-Data-Provider)                       | [broadinstitute/molecular-data-provider](https://github.com/broadinstitute/molecular-data-provider)             |
-| [Service Provider](../../teams/service-provider.md)        | BioThings                           | [Service Provider Page](service-provider.md)                                                                                                                                | [biothings/BioThings_Explorer_TRAPI](https://github.com/biothings/BioThings_Explorer_TRAPI)                     |
+| [Service Provider](../../teams/service-provider.md)        | BioThings                           | [Service Provider Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Service-Provider)                                                                                                                                | [biothings/BioThings_Explorer_TRAPI](https://github.com/biothings/BioThings_Explorer_TRAPI)                     |
 | Text Mining Provider    | Text Mining Provider                | [Targeted Text-Mined Association KG Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Targeted-Text-Mined-Association-KG) | [NCATSTranslator/Text-Mining-Provider-Roadmap](https://github.com/NCATSTranslator/Text-Mining-Provider-Roadmap) |
 | Clinical Data Provider  | Columbia Open Health Data ('COHD')  | [COHD KP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/COHD-KP)                                                       |                                                                                                                 |
 | Clinical Data Provider  | OpenPredict                         | [OpenPredict KP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/OpenPredict-KP)                                         |                                                                                                                 |
 | Clinical Data Provider  | Knowledge Collaboratory             | [Knowledge Collaboratory KP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Knowledge-Collaboratory-KP)                 |                                                                                                                 |
 | Multiomics Provider     | BigGIM II-DrugResponse              | [BigGIM II-DrugResponse Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Big-GIM-II:-Drug-Response-KP)                   |                                                                                                                                                                                                |
 | Multiomics Provider     | Multiomics Wellness                 | [Multiomics Wellness Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Wellness-KP)                                       |                                                                                                                 |
 | Multiomics Provider     | EHR Clinical Risk                   | [EHR Clinical Risk Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP)                                         |                                                                                                                 |
-| Multiomics Provider     | Clinical Trials                     | [ClinicalTrials KP](https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP)                 | [ClinicalTrials_KP](https://github.com/multiomicsKP/clinical_trials_kp)         |
-| Multiomics Provider     | Drug Approvals                     | [Drug Approvals KP](https://github.com/NCATSTranslator/Translator-All/wiki/Multiomics-Drug-Approvals-KP)                 | [Drug Approvals KP](https://github.com/multiomicsKP/drug_approvals_kp)         |
-| Expander Agent          | RTX-KG2                             | [RTX-KG2 Page](rtx-kg2.md)<br/>[RTX-KG2 Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/KG2)                            | [RTXteam/RTX-KG2](https://github.com/RTXteam/RTX-KG2)                                                           |
+| Multiomics Provider     | Clinical Trials                     | [ClinicalTrials Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP)                 |         |
+| Multiomics Provider     | Drug Approvals                     | [Drug Approvals Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Multiomics-Drug-Approvals-KP)                 |      |
+| Expander Agent          | RTX-KG2                             |[RTX-KG2 Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/KG2)                            | [RTXteam/RTX-KG2](https://github.com/RTXteam/RTX-KG2)                                                           |
 | [Service Provider](../../teams/service-provider.md)        | Pathway Figure OCR                  | [Pathway Figure OCR Wiki](<https://github.com/NCATSTranslator/Translator-All/wiki/Pathway-Figure-OCR-(PFOCR)>)                       | [wikipathways/pathway-figure-ocr](https://github.com/wikipathways/pathway-figure-ocr)                           |
 | Exposures Provider      | ICEES                               | [ICEES Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-ICEES)                                        | [NCATS-Tangerine/icees-api](https://github.com/NCATS-Tangerine/icees-api)                                       |
 | Exposures Provider      | Causal Activity Model (CAM) KP      | [CAM-KP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/CAM-KP)                                                         | [NCATS-Tangerine/cam-kp-api](https://github.com/NCATS-Tangerine/cam-kp-api)                                     |

diff --git a/docs/architecture/ui.md b/docs/architecture/ui.md
@@ -1,3 +1,3 @@
 # Translator User Interface
 
-The primary Translator User Interface (UI) is under development as a [web portal](https://ui.transltr.io/) to the Translator system that receives scored results and evidence, confidence, and provenance from the ARS and exposes results to users. This section doesn't cover the use of the UI, but rather, technical details facilitating its further development and maintenance.
+The [Translator User Interface (UI)](https://ui.transltr.io/) is under development as the primary access point to the Translator system. The UI receives scored results and evidence, confidence, and provenance from the ARS and exposes results to users. This section isn't intended to cover the use of the UI, but rather, technical details facilitating its further development and maintenance.
diff --git a/docs/deployment-guide/ci.md b/docs/deployment-guide/ci.md
@@ -1,3 +1 @@
-# Continuous Integration (CI) Testing of the Translator System
 
-T.B.A. (Mark Williams)
diff --git a/docs/deployment-guide/deployment.md b/docs/deployment-guide/deployment.md
@@ -1,3 +1,3 @@
 # Deployment
 
-T.B.A. (Mark Williams)
+T.B.A. (Sarah Stemann)
diff --git a/docs/deployment-guide/index.md b/docs/deployment-guide/index.md
@@ -2,6 +2,5 @@
 
 This section of the Translator technical documentation provides details mainly of interest to system administrators and development operations teams deploying, and monitoring the ongoing performance of, the Translator system in a production environment.
 
-* [Continuous Integration Processes for Translator](ci.md)
 * [Deploying Components to Production](deployment.md)
 * [Monitoring the Translator System](monitoring.md)
diff --git a/docs/development-guide/tutorials/consortium_development_guidelines.md b/docs/development-guide/tutorials/consortium_development_guidelines.md
@@ -1,30 +1 @@
-# Consortium Development Guidelines
 
-1. Project Management
-   1. Project Management in Translator
-      1. Project milestones
-   2. Github in Translator
-      1. Setting up repositories
-         1. Role of NCATSTranslator, and other related specialized Git Organizations
-         2. User Groups
-         3. Access Policies
-      2. Forking code
-      3. Issue tracking
-      4. How to submit a project GitHub Pull Request (PR)
-      5. Publishing releases
-      6. Publishing modules (pypi)
-2. Coding process - Tim, Chris B
-   1. Test Driven development
-   2. Documentation Requirements
-      1. Licensing
-3. Describe how to test, deploy & version artifacts
-   1. Versioning artifacts
-   2. Component registration: Translator Smart API Registry
-      1. SmartAPI translator extension metadata
-   3. Deployment environments:
-      1. x-maturity: dev, prod, etc.
-   4. Continuous Integration
-   5. Packaging
-      1. Docker
-   6. Deployment Process (DevOps)
-      1. ITRB
diff --git a/docs/faq.md b/docs/faq.md
@@ -4,7 +4,7 @@
 Check out our [introduction to knowledge graphs](architecture/biolink/knowledge_graphs.md)?
 
 ### How can I start playing with Translator?
-Translator is generally accessible to researchers via the [Translator Web portal](https://ui.transltr.io/). Python-savvy data scientists can try out the ["Hello Translator" Jupyter Notebook](development-guide/HelloTranslator.ipynb).
+Translator is accessible to translational science end users via the [Translator user interface](https://ui.transltr.io/). Python-savvy data scientists can try out the [“Hello Translator” Jupyter Notebook](development-guide/HelloTranslator.ipynb).
 
 ### How can I develop software to use and/or contribute to Translator?
 We composed a [set of tutorials](development-guide/tutorials/index.md) for you.