aiagents4pharma 1.41.0__py3-none-any.whl → 1.43.0__py3-none-any.whl

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Files changed (49) hide show
  1. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +1 -1
  2. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +37 -0
  3. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml +3 -0
  4. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml +3 -0
  5. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml +6 -0
  6. aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml +5 -0
  7. aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py +752 -350
  8. aiagents4pharma/talk2scholars/agents/paper_download_agent.py +7 -4
  9. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml +49 -95
  10. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml +15 -1
  11. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml +16 -2
  12. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +40 -5
  13. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml +15 -5
  14. aiagents4pharma/talk2scholars/configs/config.yaml +1 -3
  15. aiagents4pharma/talk2scholars/configs/tools/paper_download/default.yaml +124 -0
  16. aiagents4pharma/talk2scholars/tests/test_arxiv_downloader.py +478 -0
  17. aiagents4pharma/talk2scholars/tests/test_base_paper_downloader.py +620 -0
  18. aiagents4pharma/talk2scholars/tests/test_biorxiv_downloader.py +697 -0
  19. aiagents4pharma/talk2scholars/tests/test_medrxiv_downloader.py +534 -0
  20. aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py +22 -12
  21. aiagents4pharma/talk2scholars/tests/test_paper_downloader.py +545 -0
  22. aiagents4pharma/talk2scholars/tests/test_pubmed_downloader.py +1067 -0
  23. aiagents4pharma/talk2scholars/tools/paper_download/__init__.py +2 -4
  24. aiagents4pharma/talk2scholars/tools/paper_download/paper_downloader.py +457 -0
  25. aiagents4pharma/talk2scholars/tools/paper_download/utils/__init__.py +20 -0
  26. aiagents4pharma/talk2scholars/tools/paper_download/utils/arxiv_downloader.py +209 -0
  27. aiagents4pharma/talk2scholars/tools/paper_download/utils/base_paper_downloader.py +343 -0
  28. aiagents4pharma/talk2scholars/tools/paper_download/utils/biorxiv_downloader.py +321 -0
  29. aiagents4pharma/talk2scholars/tools/paper_download/utils/medrxiv_downloader.py +198 -0
  30. aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py +337 -0
  31. aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +97 -45
  32. aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +47 -29
  33. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.43.0.dist-info}/METADATA +30 -14
  34. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.43.0.dist-info}/RECORD +38 -30
  35. aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml +0 -4
  36. aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py +0 -3
  37. aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml +0 -2
  38. aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py +0 -3
  39. aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml +0 -2
  40. aiagents4pharma/talk2scholars/tests/test_paper_download_biorxiv.py +0 -151
  41. aiagents4pharma/talk2scholars/tests/test_paper_download_medrxiv.py +0 -151
  42. aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py +0 -249
  43. aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py +0 -177
  44. aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py +0 -114
  45. aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py +0 -114
  46. /aiagents4pharma/talk2scholars/configs/tools/{download_arxiv_paper → paper_download}/__init__.py +0 -0
  47. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.43.0.dist-info}/WHEEL +0 -0
  48. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.43.0.dist-info}/licenses/LICENSE +0 -0
  49. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.43.0.dist-info}/top_level.txt +0 -0
aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml CHANGED
@@ -60,4 +60,4 @@ milvus_db:
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  collection_nodes_drug: "t2kg_primekg_nodes_drug"
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  collection_nodes_disease: "t2kg_primekg_nodes_disease"
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  query_batch_size: 1000000
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- cache_edge_index_path: "aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl"
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+ cache_edge_index_path: "${oc.env:CACHE_EDGE_INDEX_PATH,aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl}"
aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml ADDED
@@ -0,0 +1,37 @@
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+ _target_: talk2knowledgegraphs.tools.multimodal_subgraph_extraction
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+ ollama_embeddings:
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+ - "nomic-embed-text"
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+ temperature: 0.1
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+ streaming: False
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+ topk: 15
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+ topk_e: 15
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+ cost_e: 0.5
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+ c_const: 0.01
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+ root: -1
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+ num_clusters: 1
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+ pruning: "gw"
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+ verbosity_level: 0
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+ search_metric_type: "IP" # Inner Product
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+ node_id_column: "node_id"
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+ node_attr_column: "node_attr"
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+ edge_src_column: "edge_src"
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+ edge_attr_column: "edge_attr"
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+ edge_dst_column: "edge_dst"
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+ node_colors_dict:
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+ "gene/protein": "#6a79f7"
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+ "molecular_function": "#82cafc"
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+ "cellular_component": "#3f9b0b"
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+ "biological_process": "#c5c9c7"
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+ "drug": "#c4a661"
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+ "disease": "#80013f"
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+
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+ biobridge:
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+ # source: "aiagents4pharma/talk2knowledgegraphs/tests/files/ibd_biobridge_multimodal/"
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+ source: "/mnt/blockstorage/biobridge_multimodal/"
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+ node_type:
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+ - "gene/protein"
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+ - "molecular_function"
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+ - "cellular_component"
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+ - "biological_process"
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+ - "drug"
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+ - "disease"
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml ADDED
@@ -0,0 +1,3 @@
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+ _target_: talk2knowledgegraphs.utils.ols_terms
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+ base_url: https://www.ebi.ac.uk/ols4/api/terms/
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml ADDED
@@ -0,0 +1,3 @@
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+ _target_: talk2knowledgegraphs.utils.reactome_pathways
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+ base_url: https://reactome.org/ContentService/data/query/
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml ADDED
@@ -0,0 +1,6 @@
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+ _target_: talk2knowledgegraphs.utils.enrichments.uniprot_proteins
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+ uniprot_url: https://www.ebi.ac.uk/proteins/api/proteins
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+ reviewed: true
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+ isoform: 0
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+ organism: Homo sapiens
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml ADDED
@@ -0,0 +1,5 @@
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+ _target_: talk2knowledgegraphs.utils.pubchem_utils
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+ pubchem_cid_base_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sourceid/
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+ pubchem_cid_description_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/
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+ pubchem_casrn2cid_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/xref/RN/
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+ pubchem_cid2smiles_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/