code synchronize

.gitignore

@@ -17,3 +17,9 @@ __pycache__
 htmlcov/
 coverage.xml
 .coverage
+
+temp
+notebooks/PathFinder_testing_results/
+notebooks/Test/
+dist/
+notebooks/PathFinder_results/

Makefile

@@ -10,11 +10,11 @@ test:
 
 # Run spell checking
 spell:
-	uv run codespell --skip=metaData,notebooks,htmlcov --ignore-words-list=EHR
+	uv run codespell --skip=metaData,notebooks,htmlcov,*.json --ignore-words-list=EHR
 
 # Run spell checking interactively (allows fixing)
 spell-fix:
-	uv run codespell --interactive 3 --skip=metaData,notebooks,htmlcov --ignore-words-list=EHR
+	uv run codespell --interactive 3 --skip=metaData,notebooks,htmlcov,*.json --ignore-words-list=EHR
 
 # Run linting
 lint:
@@ -47,4 +47,4 @@ help:
 	@echo "  lint-notebooks - Run code linting on notebooks (informational)"
 	@echo "  format   - Format code"
 	@echo "  check    - Run all checks (lint, spell, test)"
-	@echo "  help     - Show this help message"
+	@echo "  help     - Show this help message"

README.md

@@ -3,15 +3,24 @@ Introduction
 
 ## What is TCT?
 Translator Component Toolkit is a python library that allowing users to explore and use KGs in the Translator ecosystem.
-Users can check out the key function documentations here: https://ncatstranslator.github.io/Translator_component_toolkit/ 
+Users can check out the key function documentations here: [https://ncatstranslator.github.io/Translator_component_toolkit/](https://ncatstranslator.github.io/Translator_component_toolkit/) 
+
+[TCT Github repo](https://github.com/NCATSTranslator/Translator_component_toolkit/tree/main)
 
 ## Key features for TCT
 Allowing users to select APIs, predicates according to the user's intention. <br>
 Parallel and fast querying of the selected APIs.<br>
 Providing reproducible results by setting constraints.<br>
-Allowing testing whether a user defined API follows a [TRAPI](https://github.com/NCATSTranslator/ReasonerAPI) standard or not. <br>
 Faciliting to explore knowledge graphs from both Translator ecosystem and user defined APIs.<br>
 Connecting large language models to convert user's questions into TRAPI queries. <br>
+Find the identifier given a name using name resolver<br>
+Annotate a node using node annotator<br>
+Explore knowledge graphs in Translator<br>
+Find neighbors in the Translator KGs for a given node <br>
+Find paths between node A and node B in the Translator KG <br>
+Find a subnetwork given a list of nodes in the Translator KG <br>
+Connecting user's API with Translator API <br>
+
 
 ## How to use TCT
 
@@ -21,6 +30,7 @@ To install TCT as a python library:
 
 ```bash
 pip install TCT
+# TCT is in development, to get the most recent update, user can install it throught the github repo
 ```
 
 **This the recommended approach for installation.**
@@ -30,59 +40,61 @@ pip install TCT
 
 The TCT is continuously updated, if you would like to use the latest functions, you can clone this repository and install it in development mode:
 
-**Using UV (recommended for development):**
+
+
+**Using pip: (recommended for development)**
 ```bash
 git clone https://github.com/NCATSTranslator/Translator_component_toolkit.git
 cd Translator_component_toolkit
-uv sync
+pip install -e .
 ```
 
-**Using pip:**
+**Using UV :**
 ```bash
 git clone https://github.com/NCATSTranslator/Translator_component_toolkit.git
 cd Translator_component_toolkit
-pip install -e .
+uv sync
 ```
 
 #### Building and Deployment
+**Using pip:**
+- Build: `python -m build`
+- Install dependencies: `pip install -e .`
 
 **Using UV:**
 - Build: `uv build`
 - Install dependencies: `uv sync`
 - Run in UV environment: `uv run python your_script.py`
 
-**Using pip:**
-- Build: `python -m build`
-- Install dependencies: `pip install -e .`
-
 
 ### Please follow the example notebooks (four utilities) below to explore the Translator APIs.
 
 #### KG overview
-Explore different KGs **[KG overview](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/overview_of_KGs.ipynb)**
+Explore different KGs **[KG overview](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/overview_of_KGs.ipynb)**
 
 #### Name Resolver and Node Normalizer
-Example notebook for **[Name Resolver and Node Normalizer](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/name_resolver_lookup.ipynb)**
+Example notebook for **[Name Resolver and Node Normalizer](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/name_resolver_lookup.ipynb)**
 
 #### Neighborhood finder
-Example notebook for **[NeighborhoodFinder](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/Neighborhood_finder.ipynb)**
+Example notebook for **[NeighborhoodFinder](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/Neighborhood_finder.ipynb)**
 
 #### Path finder
-Example notebook for **[PathFinder](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/Path_finder.ipynb)**
+Example notebook for **[PathFinder](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/Path_finder.ipynb)**
 
 #### Network finder
-Example notebook for **[NetworkFinder](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/Network_finder.ipynb)**
+Example notebook for **[NetworkFinder](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/Neighborhood_finder_multiple_nodes.ipynb)**
 
-#### Translate users' questions into TRAPI queries
-Example notebook for translating users' questions into TRAPI queries can be found [here](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/Question2Query_chatGPT.ipynb). 
 
 #### Connecting to a user's API
 API should be developed following the standard from [TRAPI](https://github.com/NCATSTranslator/ReasonerAPI). <br>
-An example notebook for add a user's API can be found [here](https://github.com/gloriachin/Translator_component_toolkit/tree/main/notebooks/Connecting_userAPI.ipynb).<br>
-**Warning: It does not work if no user' API is established**<br>
+An example notebook for add a user's API can be found [here](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/Connecting_userAPI.ipynb).<br>
+**Note: It does not work if no user' API is established**<br>
+
+### Visulize the results
+After each pipleline, it will generate a result file for visualization. A user can use **[the Visualization html](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/visulize_path_finder_results.html)** file to visulaize the results.
 
 ## Key Translator components
-Connecting to key Translator components can be found [here](https://github.com/gloriachin/Translator_component_toolkit/tree/main/TranslatorComponentsIntroduction.md)
+Connecting to key Translator components can be found [here](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/TranslatorComponentsIntroduction.md)
 
 ### Contributing
 TCT is a tool that helps to explore knowledge graphs developed in the Biomedical Data Translator Consortium. Consortium members and external contributors are encouraged to submit issues and pull requests.