aiagents4pharma 1.41.0__tar.gz → 1.43.0__tar.gz

{aiagents4pharma-1.41.0 → aiagents4pharma-1.43.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.41.0
+Version: 1.43.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -65,20 +65,37 @@ Requires-Dist: plotly-express==0.4.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: scanpy==1.11.0
 Requires-Dist: openpyxl==3.1.5
-Requires-Dist: pymilvus==2.5.11
 Dynamic: license-file
 
+<img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
+
+<!--  Project Info -->
+
+![RELEASE](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=RELEASE)
+![Docker Compose Release Version](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=Docker%20Compose%20Version)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+<!--  Deployment Workflows -->
+
+[![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
+[![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
+
+<!--  Tests -->
+
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
 [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
-[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
-[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
-![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
-![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
-![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+
+<!--  Docker Pulls -->
+
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
 
 ## Introduction
 
@@ -170,14 +187,13 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 To use the **Agents**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
 
-**Talk2Scholars** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
+**Talk2Scholars** and **Talk2KnowledgeGraphs** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
 
+> By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
+> To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
 > Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.
 > You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
 
-📝 By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.  
-To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
-
 **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
 
 _Please note that this will create a new tracing project in your Langsmith

{aiagents4pharma-1.41.0 → aiagents4pharma-1.43.0}/README.md

@@ -1,14 +1,32 @@
+<img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
+
+<!--  Project Info -->
+
+![RELEASE](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=RELEASE)
+![Docker Compose Release Version](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=Docker%20Compose%20Version)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+<!--  Deployment Workflows -->
+
+[![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
+[![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
+
+<!--  Tests -->
+
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
 [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
-[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
-[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
-![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
-![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
-![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
-![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+
+<!--  Docker Pulls -->
+
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
 
 ## Introduction
 
@@ -100,14 +118,13 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 To use the **Agents**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
 
-**Talk2Scholars** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
+**Talk2Scholars** and **Talk2KnowledgeGraphs** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
 
+> By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
+> To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
 > Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.
 > You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
 
-📝 By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.  
-To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
-
 **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
 
 _Please note that this will create a new tracing project in your Langsmith

{aiagents4pharma-1.41.0 → aiagents4pharma-1.43.0}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml

@@ -60,4 +60,4 @@ milvus_db:
   collection_nodes_drug: "t2kg_primekg_nodes_drug"
   collection_nodes_disease: "t2kg_primekg_nodes_disease"
   query_batch_size: 1000000
-  cache_edge_index_path: "aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl"
+  cache_edge_index_path: "${oc.env:CACHE_EDGE_INDEX_PATH,aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl}"

aiagents4pharma-1.43.0/aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml

@@ -0,0 +1,37 @@
+_target_: talk2knowledgegraphs.tools.multimodal_subgraph_extraction
+ollama_embeddings:
+  - "nomic-embed-text"
+temperature: 0.1
+streaming: False
+topk: 15
+topk_e: 15
+cost_e: 0.5
+c_const: 0.01
+root: -1
+num_clusters: 1
+pruning: "gw"
+verbosity_level: 0
+search_metric_type: "IP"  # Inner Product
+node_id_column: "node_id"
+node_attr_column: "node_attr"
+edge_src_column: "edge_src"
+edge_attr_column: "edge_attr"
+edge_dst_column: "edge_dst"
+node_colors_dict:
+  "gene/protein": "#6a79f7"
+  "molecular_function": "#82cafc"
+  "cellular_component": "#3f9b0b"
+  "biological_process": "#c5c9c7"
+  "drug": "#c4a661"
+  "disease": "#80013f"
+
+biobridge:
+  # source: "aiagents4pharma/talk2knowledgegraphs/tests/files/ibd_biobridge_multimodal/"
+  source: "/mnt/blockstorage/biobridge_multimodal/"
+  node_type:
+    - "gene/protein"
+    - "molecular_function"
+    - "cellular_component"
+    - "biological_process"
+    - "drug"
+    - "disease"

aiagents4pharma-1.43.0/aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml

@@ -0,0 +1,3 @@
+_target_: talk2knowledgegraphs.utils.ols_terms
+base_url: https://www.ebi.ac.uk/ols4/api/terms/
+timeout: 10

aiagents4pharma-1.43.0/aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml

@@ -0,0 +1,3 @@
+_target_: talk2knowledgegraphs.utils.reactome_pathways
+base_url: https://reactome.org/ContentService/data/query/
+timeout: 10

aiagents4pharma-1.43.0/aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml

@@ -0,0 +1,6 @@
+_target_: talk2knowledgegraphs.utils.enrichments.uniprot_proteins
+uniprot_url: https://www.ebi.ac.uk/proteins/api/proteins
+reviewed: true
+isoform: 0
+organism: Homo sapiens
+timeout: 10

aiagents4pharma-1.43.0/aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml

@@ -0,0 +1,5 @@
+_target_: talk2knowledgegraphs.utils.pubchem_utils
+pubchem_cid_base_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sourceid/
+pubchem_cid_description_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/
+pubchem_casrn2cid_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/xref/RN/
+pubchem_cid2smiles_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/