--- a
+++ b/mkdocs.yml
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+site_name: AIAgents4Pharma
+
+nav:
+  - Home: index.md
+
+  - Talk2AIAgents4Pharma:
+      - Introduction: talk2aiagents4pharma/intro.md
+      - Agents:
+          - T2AA4P agent: talk2aiagents4pharma/agents/main_agent.md
+      - States:
+          - T2AA4P state: talk2aiagents4pharma/states/state_talk2aiagents4pharma.md
+
+  - Talk2Biomodels:
+      - Introduction: talk2biomodels/intro.md
+      - FAQ: talk2biomodels/faq.md
+      - Case Studies:
+          - Precision medicine: talk2biomodels/cases/Case_1.md
+          - Epidemiology: talk2biomodels/cases/Case_2.md
+          - Emergent system properties: talk2biomodels/cases/Case_3.md
+      - Tutorials:
+          - ./notebooks/talk2biomodels/tutorial_load_model.ipynb
+          - ./notebooks/talk2biomodels/example_models.md
+      - Agents:
+          - T2B agent: talk2biomodels/agents/t2b_agent.md
+      - States:
+          - T2B state: talk2biomodels/states/state_talk2biomodels.md
+      - Models:
+          - System Bio Model: talk2biomodels/models/sys_bio_model.md
+          - Basico Model: talk2biomodels/models/basico_model.md
+      - Tools:
+          - Search models: talk2biomodels/tools/search_models.md
+          - Model information: talk2biomodels/tools/get_modelinfo.md
+          - Simulate model: talk2biomodels/tools/simulate_model.md
+          - Ask questions: talk2biomodels/tools/ask_question.md
+          - Custom plots: talk2biomodels/tools/custom_plotter.md
+          - Load biomodel: talk2biomodels/tools/load_biomodel.md
+
+  - Talk2Cells:
+      - Talk2Cells: talk2cells/intro.md
+      - Tutorials:
+          - Cell Annotation: ./notebooks/talk2cells/tutorial_cell_annotation.ipynb
+          - Cell Discovery: ./notebooks/talk2cells/tutorial_cell_discovery.ipynb
+          - UMAP Visualization: ./notebooks/talk2cells/tutorial_UMAP_visualization.ipynb
+          - Cell Type Proportion: ./notebooks/talk2cells/tutorial_cell_type_proportion.ipynb
+      - Agents:
+          - SCP Agent: talk2cells/agents/scp_agent.md
+      - States:
+          - Talk2Cells: talk2cells/states/state_talk2cells.md
+      - Tools:
+          - Search studies: talk2cells/tools/search_studies.md
+          - Display studies: talk2cells/tools/display_studies.md
+
+  - Talk2KnowledgeGraphs:
+      - Introduction: talk2knowledgegraphs/intro.md
+      - Tutorials:
+          - PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_primekg_loader.ipynb
+          - StarkQA-PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_loader.ipynb
+          - BioBridge-PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_primekg_loader.ipynb
+          - PrimeKG Subgraph Extraction: ./notebooks/talk2knowledgegraphs/tutorial_primekg_subgraph.ipynb
+          - Textual Embeddings (all-minilm): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_textual_embeddings_all_minilm.ipynb
+          - Textual Embeddings (nomic-embed-text): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_textual_embeddings_nomic_embed_text.ipynb
+          - Drug Enrichments/Embeddings (SMILES/molmim): ./notebooks/talk2knowledgegraphs/tutorial_primekg_smiles_enrich_embed.ipynb
+          - Protein Embeddings: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_primekg_protein_embeddings.ipynb
+          - Embedding Alignment: ./notebooks/talk2knowledgegraphs/tutorial_multimodal_embeddings_alignment.ipynb
+          - Evaluation (VSS): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_evaluation_vss.ipynb
+          - Talk2KG Agentic Tools: ./notebooks/talk2knowledgegraphs/tutorial_talk2kg_agentic_tools.ipynb
+          - PyG2DataFrame: ./notebooks/talk2knowledgegraphs/tutorial_pyg2dataframe.ipynb
+          - UniProt ID Mapping: ./notebooks/talk2knowledgegraphs/tutorial_uniprot_mapping.ipynb
+      - Datasets:
+          - Dataset: talk2knowledgegraphs/datasets/dataset.md
+          - PrimeKG: talk2knowledgegraphs/datasets/primekg.md
+          - StarkQA-PrimeKG: talk2knowledgegraphs/datasets/starkqa_primekg.md
+          - BioBridge-PrimeKG: talk2knowledgegraphs/datasets/biobridge_primekg.md
+      - Utils:
+          - Embeddings:
+              - Embeddings: talk2knowledgegraphs/utils/embeddings/embeddings.md
+              - EmbeddingWithSentenceTransformer: talk2knowledgegraphs/utils/embeddings/sentence_transformer.md
+              - EmbeddingWithHuggingFace: talk2knowledgegraphs/utils/embeddings/huggingface.md
+              - EmbeddingWithOllama: talk2knowledgegraphs/utils/embeddings/ollama.md
+              - EmbeddingWithMOLMIM: talk2knowledgegraphs/utils/embeddings/nim_molmim.md
+          - Enrichments:
+              - Enrichments: talk2knowledgegraphs/utils/enrichments/enrichments.md
+              - EnrichmentWithOllama: talk2knowledgegraphs/utils/enrichments/ollama.md
+              - EnrichmentWithPubChem: talk2knowledgegraphs/utils/enrichments/pubchem_strings.md
+      - Agents:
+          - Talk2KG Agent: talk2knowledgegraphs/agents/t2kg_agent.md
+      - States:
+          - Talk2KG State: talk2knowledgegraphs/states/state_talk2knowledgegraphs.md
+      - Tools:
+          - Subgraph Extraction: talk2knowledgegraphs/tools/subgraph_extraction.md
+          - Subgraph Summarization: talk2knowledgegraphs/tools/subgraph_summarization.md
+          - GraphRAG Reasoning: talk2knowledgegraphs/tools/graphrag_reasoning.md
+          - Load Arguments: talk2knowledgegraphs/tools/load_arguments.md
+
+  - Talk2Scholars:
+      - Introduction: talk2scholars/intro.md
+      - Tutorials: ./notebooks/talk2scholars/tutorial.ipynb
+      - Agents:
+          - Main Agent: talk2scholars/agents/main_agent.md
+          - S2 Agent: talk2scholars/agents/s2_agent.md
+          - Paper Download Agent: talk2scholars/agents/paper_download_agent.md
+          - Zotero Agent: talk2scholars/agents/zotero_agent.md
+          - PDF Agent: talk2scholars/agents/pdf_agent.md
+      - States:
+          - Talk2Scholars state: talk2scholars/states/state_talk2scholars.md
+      - Tools:
+          - Search papers: talk2scholars/tools/search.md
+          - Single paper recommendation: talk2scholars/tools/single_paper_rec.md
+          - Multi paper recommendation: talk2scholars/tools/multi_paper_rec.md
+          - Display results: talk2scholars/tools/display_results.md
+          - Query results: talk2scholars/tools/query_results.md
+          - Retrieve ID: talk2scholars/tools/retrieve_semantic_scholar_paper_id.md
+          - Download Arxiv Input: talk2scholars/tools/download_arxiv_input.md
+          - Arxiv Downloader: talk2scholars/tools/arxiv_downloader.md
+          - Abstract Downloader: talk2scholars/tools/abstract_downloader.md          
+          - Zotero Read: talk2scholars/tools/zotero_read.md
+          - Question and answer: talk2scholars/tools/question_and_answer.md
+
+  - Documentation:
+      - Ops:
+          - Introduction: ops/Documentation_intro.md
+          - CodeOps: ops/CodeOps.md
+          - DevOps: ops/DevOps.md
+      - Contributing:
+          - Contributing: CONTRIBUTING.md
+
+repo_url: https://github.com/VirtualPatientEngine/AIAgents4Pharma
+repo_name: VPE/AIAgents4Pharma
+
+extra_css:
+  - VPE.png
+theme:
+  name: material
+  logo: assets/VPE.png
+  palette:
+    - accent: black
+      primary: white
+      scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline
+        name: Switch to dark mode
+    - accent: black
+      primary: white
+      scheme: slate
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode
+  features:
+    - navigation.top
+    - navigation.tabs
+    - navigation.instant
+    - navigation.expand
+    - search.suggest
+    - search.highlight
+    - content.code.copy
+    - navigation.scrollable
+
+plugins:
+  - search:
+      lang:
+        - en
+        - de
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            filters: None
+  - mkdocs-jupyter:
+      include_source: True
+  - tags
+  - include-markdown
+
+markdown_extensions:
+  - pymdownx.highlight
+    # anchor_linenums: true
+    # line_spans: __span
+    # pygments_lang_class: true
+  - pymdownx.superfences
+
+extra:
+  notebooks:
+    - overview.md: notebooks/overview.md