aiagents4pharma 1.32.0__py3-none-any.whl → 1.34.0__py3-none-any.whl

aiagents4pharma/talk2knowledgegraphs/configs/config.yaml

@@ -5,4 +5,7 @@ defaults:
   - tools/subgraph_summarization: default
   - tools/graphrag_reasoning: default
   - utils/pubchem_utils: default
+  - utils/enrichments/uniprot_proteins: default
+  - utils/enrichments/ols_terms: default
+  - utils/enrichments/reactome_pathways: default
   - app/frontend: default

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+"""
+Test cases for utils/enrichments/ols_terms.py
+"""
+
+import pytest
+from ..utils.enrichments.ols_terms import EnrichmentWithOLS
+
+# In this test, we will consider 5 examples:
+# 1. CL_0000899: T-helper 17 cell (Cell Ontology)
+# 2. GO_0046427: positive regulation of receptor signaling pathway via JAK-STAT (GO)
+# 3. UBERON_0000004: nose (Uberon)
+# 4. HP_0009739: Hypoplasia of the antihelix (Human Phenotype Ontology)
+# 5. MONDO_0005011: Crohn disease (MONDO)
+# 6. XYZ_0000000: Non-existing term (for testing error handling)
+
+# The expected description for each term starts with:
+CL_DESC = "CD4-positive, alpha-beta T cell"
+GO_DESC = "Any process that activates or increases the frequency, rate or extent"
+UBERON_DESC = "The olfactory organ of vertebrates, consisting of nares"
+HP_DESC = "Hypoplasia of the antihelix"
+MONDO_DESC = "A gastrointestinal disorder characterized by chronic inflammation"
+
+# The expected description for the non-existing term is None
+
+@pytest.fixture(name="enrich_obj")
+def fixture_uniprot_config():
+    """Return a dictionary with the configuration for OLS enrichment."""
+    return EnrichmentWithOLS()
+
+def test_enrich_documents(enrich_obj):
+    """Test the enrich_documents method."""
+    ols_terms = ["CL_0000899",
+                 "GO_0046427",
+                 "UBERON_0000004",
+                 "HP_0009739",
+                 "MONDO_0005011",
+                 "XYZ_0000000"]
+    descriptions = enrich_obj.enrich_documents(ols_terms)
+    assert descriptions[0].startswith(CL_DESC)
+    assert descriptions[1].startswith(GO_DESC)
+    assert descriptions[2].startswith(UBERON_DESC)
+    assert descriptions[3].startswith(HP_DESC)
+    assert descriptions[4].startswith(MONDO_DESC)
+    assert descriptions[5] is None
+
+def test_enrich_documents_with_rag(enrich_obj):
+    """Test the enrich_documents_with_rag method."""
+    ols_terms = ["CL_0000899",
+                 "GO_0046427",
+                 "UBERON_0000004",
+                 "HP_0009739",
+                 "MONDO_0005011",
+                 "XYZ_0000000"]
+    descriptions = enrich_obj.enrich_documents_with_rag(ols_terms, None)
+    assert descriptions[0].startswith(CL_DESC)
+    assert descriptions[1].startswith(GO_DESC)
+    assert descriptions[2].startswith(UBERON_DESC)
+    assert descriptions[3].startswith(HP_DESC)
+    assert descriptions[4].startswith(MONDO_DESC)
+    assert descriptions[5] is None

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py

@@ -13,7 +13,9 @@ from ..utils.enrichments.pubchem_strings import EnrichmentWithPubChem
 # The expected SMILES representation for the first PubChem ID is:
 SMILES_FIRST = 'C[C@@H]1C[C@H]2[C@@H]3[C@@H](CC4=CC(=O)C=C[C@@]'
 SMILES_FIRST += '4([C@H]3[C@H](C[C@@]2([C@]1(C(=O)CO)O)C)O)C)Cl'
-# The expected SMILES representation for the second PubChem ID is None.
+# The expected description for the first PubChem ID starts with:
+DESCRIPTION_FIRST = "Alclometasone is a prednisolone compound having an alpha-chloro substituent"
+# The expected SMILES representation and description for the second PubChem ID is None.
 
 @pytest.fixture(name="enrich_obj")
 def fixture_pubchem_config():
@@ -23,11 +25,16 @@ def fixture_pubchem_config():
 def test_enrich_documents(enrich_obj):
     """Test the enrich_documents method."""
     pubchem_ids = ["5311000", "1X"]
-    enriched_strings = enrich_obj.enrich_documents(pubchem_ids)
+    enriched_descriptions, enriched_strings = enrich_obj.enrich_documents(pubchem_ids)
     assert enriched_strings == [SMILES_FIRST, None]
+    assert enriched_descriptions[0].startswith(DESCRIPTION_FIRST)
+    assert enriched_descriptions[1] is None
 
 def test_enrich_documents_with_rag(enrich_obj):
     """Test the enrich_documents_with_rag method."""
     pubchem_ids = ["5311000", "1X"]
-    enriched_strings = enrich_obj.enrich_documents_with_rag(pubchem_ids, None)
+    enriched_descriptions, enriched_strings = enrich_obj.enrich_documents_with_rag(pubchem_ids,
+                                                                                   None)
     assert enriched_strings == [SMILES_FIRST, None]
+    assert enriched_descriptions[0].startswith(DESCRIPTION_FIRST)
+    assert enriched_descriptions[1] is None

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+"""
+Test cases for utils/enrichments/reactome_pathways.py
+"""
+
+import pytest
+from ..utils.enrichments.reactome_pathways import EnrichmentWithReactome
+
+# In this test, we will consider 2 examples:
+# 1. R-HSA-3244647: cGAS binds cytosolic DNA
+# 2. R-HSA-9905952: ATP binds P2RX7 in P2RX7 trimer:PANX1 heptamer
+# 3. R-HSA-1234567: Fake pathway
+
+# The expected description of pathway R-HSA-3244647 startswith:
+FIRST_PATHWAY = "Cyclic GMP-AMP (cGAMP) synthase (cGAS) was identified as a cytosolic DNA"
+# The expected description of pathway R-HSA-9905952 startswith:
+SECOND_PATHWAY = "The P2RX7 (P2X7, P2Z) trimer binds ATP,"
+# The expected description of pathway R-HSA-1234567 is None.
+
+@pytest.fixture(name="enrich_obj")
+def fixture_uniprot_config():
+    """Return a dictionary with the configuration for Reactome enrichment."""
+    return EnrichmentWithReactome()
+
+def test_enrich_documents(enrich_obj):
+    """Test the enrich_documents method."""
+    reactome_pathways = ["R-HSA-3244647",
+                         "R-HSA-9905952",
+                         "R-HSA-1234567"]
+    descriptions = enrich_obj.enrich_documents(reactome_pathways)
+    assert descriptions[0].startswith(FIRST_PATHWAY)
+    assert descriptions[1].startswith(SECOND_PATHWAY)
+    assert descriptions[2] is None
+
+def test_enrich_documents_with_rag(enrich_obj):
+    """Test the enrich_documents_with_rag method."""
+    reactome_pathways = ["R-HSA-3244647",
+                         "R-HSA-9905952",
+                         "R-HSA-1234567"]
+    descriptions = enrich_obj.enrich_documents_with_rag(reactome_pathways, None)
+    assert descriptions[0].startswith(FIRST_PATHWAY)
+    assert descriptions[1].startswith(SECOND_PATHWAY)
+    assert descriptions[2] is None

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+"""
+Test cases for utils/enrichments/uniprot_proteins.py
+"""
+
+import pytest
+from ..utils.enrichments.uniprot_proteins import EnrichmentWithUniProt
+
+# In this test, we will consider 2 examples:
+# 1. Gene Name: TP53
+# 2. Gene Name: TP5 (Incomplete; must return empty results)
+# 2. Gene Name: XZ (Shorter than 3 characters; must return empty results)
+# The expected description of TP53 startswith:
+START_DESCP = "Multifunctional transcription factor"
+# The expected amino acid sequence of TP53 startswith:
+START_SEQ = "MEEPQSDPSV"
+
+@pytest.fixture(name="enrich_obj")
+def fixture_uniprot_config():
+    """Return a dictionary with the configuration for UniProt enrichment."""
+    return EnrichmentWithUniProt()
+
+def test_enrich_documents(enrich_obj):
+    """Test the enrich_documents method."""
+    gene_names = ["TP53", "TP5", "XZ"]
+    descriptions, sequences = enrich_obj.enrich_documents(gene_names)
+    assert descriptions[0].startswith(START_DESCP)
+    assert sequences[0].startswith(START_SEQ)
+    assert descriptions[1] is None
+    assert sequences[1] is None
+    assert descriptions[2] is None
+    assert sequences[2] is None
+
+def test_enrich_documents_with_rag(enrich_obj):
+    """Test the enrich_documents_with_rag method."""
+    gene_names = ["TP53", "TP5", "XZ"]
+    descriptions, sequences = enrich_obj.enrich_documents_with_rag(gene_names, None)
+    assert descriptions[0].startswith(START_DESCP)
+    assert sequences[0].startswith(START_SEQ)
+    assert descriptions[1] is None
+    assert sequences[1] is None
+    assert descriptions[2] is None
+    assert sequences[2] is None

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -4,13 +4,35 @@ Test cases for utils/pubchem_utils.py
 
 from ..utils import pubchem_utils
 
-def test_drugbank_id2pubchem_cid():
+def test_external_id2pubchem_cid():
     """
-    Test the drugbank_id2pubchem_cid method.
+    Test the external_id2pubchem_cid function.
 
     The DrugBank ID for Alclometasone is DB00240.
     The PubChem CID for Alclometasone is 5311000.
+
+    The CTD ID for Butylated Hydroxyanisole is D002083
+    The PubChem CID for Butylated Hydroxyanisole is 24667.
     """
     drugbank_id = "DB00240"
-    pubchem_cid = pubchem_utils.drugbank_id2pubchem_cid(drugbank_id)
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid('drugbank', drugbank_id)
     assert pubchem_cid == 5311000
+
+    ctd_id = "D002083"
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid(
+                    'comparative toxicogenomics database',
+                    ctd_id)
+    assert pubchem_cid == 24667
+
+def test_pubchem_cid_description():
+    """
+    Test the pubchem_cid_description function.
+
+    The PubChem CID for Alclometasone is 5311000.
+    The description for Alclometasone starts with 
+        "Alclometasone is a prednisolone compound having an alpha-chloro substituent".
+    """
+    pubchem_cid = 5311000
+    description = pubchem_utils.pubchem_cid_description(pubchem_cid)
+    assert description.startswith(
+        "Alclometasone is a prednisolone compound having an alpha-chloro substituent")

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py

@@ -4,3 +4,6 @@ This package contains modules to use the enrichment model
 from . import enrichments
 from . import ollama
 from . import pubchem_strings
+from . import uniprot_proteins
+from . import reactome_pathways
+from . import ols_terms

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching OLS terms with textual descriptions
+"""
+
+from typing import List
+import logging
+import json
+import hydra
+import requests
+from .enrichments import Enrichments
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+class EnrichmentWithOLS(Enrichments):
+    """
+    Enrichment class using OLS terms
+    """
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input OLS terms
+
+        Args:
+            texts: The list of OLS terms to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+
+        ols_ids = texts
+
+        logger.log(logging.INFO,
+                   "Load Hydra configuration for OLS enrichments.")
+        with hydra.initialize(version_base=None, config_path="../../configs"):
+            cfg = hydra.compose(config_name='config',
+                                overrides=['utils/enrichments/ols_terms=default'])
+            cfg = cfg.utils.enrichments.ols_terms
+
+        descriptions = []
+        for ols_id in ols_ids:
+            params = {
+                'short_form': ols_id
+            }
+            r = requests.get(cfg.base_url,
+                             headers={ "Accept" : "application/json"},
+                             params=params,
+                             timeout=cfg.timeout)
+            response_body = json.loads(r.text)
+            # if the response body is empty
+            if '_embedded' not in response_body:
+                descriptions.append(None)
+                continue
+            # Add the description to the list
+            description = response_body['_embedded']['terms'][0]['description']
+            # Add synonyms to the description
+            description += response_body['_embedded']['terms'][0]['synonyms']
+            # Add the label to the description
+            # Label is not provided as list, so we need to convert it to a list
+            description += [response_body['_embedded']['terms'][0]['label']]
+            descriptions.append('\n'.join(description))
+        return descriptions
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input OLS terms
+
+        Args:
+            texts: The list of OLS to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+        return self.enrich_documents(texts)

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python3
 
 """
-Enrichment class for enriching PubChem IDs with their STRINGS representation.
+Enrichment class for enriching PubChem IDs with their STRINGS representation and descriptions.
 """
 
 from typing import List
 import pubchempy as pcp
 from .enrichments import Enrichments
+from ..pubchem_utils import pubchem_cid_description
 
 class EnrichmentWithPubChem(Enrichments):
     """
@@ -20,20 +21,24 @@ class EnrichmentWithPubChem(Enrichments):
             texts: The list of pubchem IDs to be enriched.
 
         Returns:
-            The list of enriched STRINGS
+            The list of enriched STRINGS and their descriptions.
         """
 
-        enriched_pubchem_ids = []
+        enriched_pubchem_ids_smiles = []
+        enriched_pubchem_ids_descriptions = []
+
         pubchem_cids = texts
         for pubchem_cid in pubchem_cids:
             try:
                 c = pcp.Compound.from_cid(pubchem_cid)
             except pcp.BadRequestError:
-                enriched_pubchem_ids.append(None)
+                enriched_pubchem_ids_smiles.append(None)
+                enriched_pubchem_ids_descriptions.append(None)
                 continue
-            enriched_pubchem_ids.append(c.isomeric_smiles)
+            enriched_pubchem_ids_smiles.append(c.isomeric_smiles)
+            enriched_pubchem_ids_descriptions.append(pubchem_cid_description(pubchem_cid))
 
-        return enriched_pubchem_ids
+        return enriched_pubchem_ids_descriptions, enriched_pubchem_ids_smiles
 
     def enrich_documents_with_rag(self, texts, docs):
         """

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching Reactome pathways with textual descriptions
+"""
+
+from typing import List
+import logging
+import hydra
+import requests
+from .enrichments import Enrichments
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+class EnrichmentWithReactome(Enrichments):
+    """
+    Enrichment class using Reactome pathways
+    """
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input Reactome pathways
+
+        Args:
+            texts: The list of Reactome pathways to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+
+        reactome_pathways_ids = texts
+
+        logger.log(logging.INFO,
+                   "Load Hydra configuration for reactome enrichment")
+        with hydra.initialize(version_base=None, config_path="../../configs"):
+            cfg = hydra.compose(config_name='config',
+                                overrides=['utils/enrichments/reactome_pathways=default'])
+            cfg = cfg.utils.enrichments.reactome_pathways
+
+        descriptions = []
+        for reactome_pathway_id in reactome_pathways_ids:
+            r = requests.get(cfg.base_url + reactome_pathway_id + '/summation',
+                             headers={ "Accept" : "text/plain"},
+                             timeout=cfg.timeout)
+            # if the response is not ok
+            if not r.ok:
+                descriptions.append(None)
+                continue
+            response_body = r.text
+            # if the response is ok
+            descriptions.append(response_body.split('\t')[1])
+        return descriptions
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input Reactome pathways
+
+        Args:
+            texts: The list of Reactome pathways to be enriched.
+
+        Returns:
+            The list of enriched descriptions
+        """
+        return self.enrich_documents(texts)

aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+
+"""
+Enrichment class for enriching Gene names with their function and sequence using UniProt.
+"""
+
+from typing import List
+import logging
+import json
+import hydra
+import requests
+from .enrichments import Enrichments
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+class EnrichmentWithUniProt(Enrichments):
+    """
+    Enrichment class using UniProt
+    """
+    def enrich_documents(self, texts: List[str]) -> List[str]:
+        """
+        Enrich a list of input UniProt gene names with their function and sequence.
+
+        Args:
+            texts: The list of gene names to be enriched.
+
+        Returns:
+            The list of enriched functions and sequences
+        """
+
+        enriched_gene_names = texts
+
+        logger.log(logging.INFO,
+                   "Load Hydra configuration for Gene enrichment with description and sequence.")
+        with hydra.initialize(version_base=None, config_path="../../configs"):
+            cfg = hydra.compose(config_name='config',
+                                overrides=['utils/enrichments/uniprot_proteins=default'])
+            cfg = cfg.utils.enrichments.uniprot_proteins
+
+
+        descriptions = []
+        sequences = []
+        for gene in enriched_gene_names:
+            params = {
+                "reviewed": cfg.reviewed,
+                "isoform": cfg.isoform,
+                "exact_gene": gene,
+                "organism": cfg.organism,
+                # You can get the list of all available organisms here:
+                # https://www.uniprot.org/help/taxonomy
+            }
+
+            r = requests.get(cfg.uniprot_url,
+                             headers={ "Accept" : "application/json"},
+                             params=params,
+                             timeout=cfg.timeout)
+            # if the response is not ok
+            if not r.ok:
+                descriptions.append(None)
+                sequences.append(None)
+                continue
+            response_body = json.loads(r.text)
+            # if the response body is empty
+            if not response_body:
+                descriptions.append(None)
+                sequences.append(None)
+                continue
+            description = ''
+            for comment in response_body[0]['comments']:
+                if comment['type'] == 'FUNCTION':
+                    for value in comment['text']:
+                        description += value['value']
+            sequence = response_body[0]['sequence']['sequence']
+            descriptions.append(description)
+            sequences.append(sequence)
+        return descriptions, sequences
+
+    def enrich_documents_with_rag(self, texts, docs):
+        """
+        Enrich a list of input UniProt gene names with their function and sequence.
+
+        Args:
+            texts: The list of gene names to be enriched.
+
+        Returns:
+            The list of enriched functions and sequences
+        """
+        return self.enrich_documents(texts)

aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py

@@ -12,12 +12,16 @@ import hydra
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def drugbank_id2pubchem_cid(drugbank_id):
+def external_id2pubchem_cid(db, db_id):
     """
-    Convert DrugBank ID to PubChem CID.
+    Convert external DB ID to PubChem CID.
+    Please refer to the following URL for more information
+    on data sources:
+    https://pubchem.ncbi.nlm.nih.gov/sources/
 
     Args:
-        drugbank_id: The DrugBank ID of the drug.
+        db: The database name.
+        db_id: The database ID of the drug.
 
     Returns:
         The PubChem CID of the drug.
@@ -28,7 +32,7 @@ def drugbank_id2pubchem_cid(drugbank_id):
                             overrides=['utils/pubchem_utils=default'])
         cfg = cfg.utils.pubchem_utils
     # Prepare the URL
-    pubchem_url_for_drug = cfg.drugbank_id_to_pubchem_cid_url + drugbank_id + '/JSON'
+    pubchem_url_for_drug = f"{cfg.pubchem_cid_base_url}/{db}/{db_id}/JSON"
     # Get the data
     response = requests.get(pubchem_url_for_drug, timeout=60)
     data = response.json()
@@ -40,3 +44,29 @@ def drugbank_id2pubchem_cid(drugbank_id):
                 cid = compound["id"].get("id", {}).get("cid")
                 break
     return cid
+
+def pubchem_cid_description(cid):
+    """
+    Get the description of a PubChem CID.
+
+    Args:
+        cid: The PubChem CID of the drug.
+
+    Returns:
+        The description of the PubChem CID.
+    """
+    logger.log(logging.INFO, "Load Hydra configuration for PubChem CID description.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['utils/pubchem_utils=default'])
+        cfg = cfg.utils.pubchem_utils
+    # Prepare the URL
+    pubchem_url_for_descpription = f"{cfg.pubchem_cid_description_url}/{cid}/description/JSON"
+    # Get the data
+    response = requests.get(pubchem_url_for_descpription, timeout=60)
+    data = response.json()
+    # Extract the PubChem CID description
+    description = ''
+    for information in data["InformationList"]['Information']:
+        description += information.get("Description", '')
+    return description

{aiagents4pharma-1.32.0.dist-info → aiagents4pharma-1.34.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.32.0
+Version: 1.34.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.32.0.dist-info → aiagents4pharma-1.34.0.dist-info}/RECORD

@@ -75,7 +75,7 @@ aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
 aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=IcXSZ2qQA1m-gS-o0Pj_g1oar8uPdhsbaovloUFka3Q,3058
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
-aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=bag4w3JCSqaojG37MTksy3ZehAPe3qoVzjIN2uh3nrc,229
+aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=X91262b-wkygiH4HrEr0bIzHxHDuDWwuxLQAmdUe-E4,367
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
 aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
@@ -111,9 +111,12 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py,sha25
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Qxo6WeIDRy8aLh1tNKw0kSlzmUj3MtTak63oW2YwB24,1327
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py,sha256=N6HRr4lWHXY7bTHe2uXJe4D_EG9WqZPibZne6qLl9_k,1447
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py,sha256=JhY7axvVULLywDJ2ctA-gob5YPeaJYWsaMNjHT6L9CU,3021
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=bk27KElJxOvKJ2RTz4ftleExQPMyWWS755KKmlImzbk,1241
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=woSm723ns9fHieu-QWFiniLlm5h22v1qzO4v6n20K5g,2413
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=0SgYvqdvxseUYTHx2KuSNI2hnmQ3VVVz0F-79_-P41o,1769
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py,sha256=r1D74mavsnSCm4xnWl0n0nM9PZqgm3doD2dulNrKNVQ,1754
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py,sha256=pal76wi7WgQWUNk56BrzfFV8jKpbDaHHdbwtgx_gXLI,2410
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=C07YqUNYW7ofpKAzKh0lBovXKLvaiXFb3oJU6k1dvu4,411
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=K1Y6QM0MDP1IrAdcWkigl8R-O-i-lsL4NCyOrWewhdM,1246
 aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=zpD4h7EYtyq0QNOqLd6bkxrPlPb2XN64ceI9ncgESrA,171
 aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py,sha256=OEuOFncDRdb7TQEGq4rkT5On-jI-R7Nt8K5EBzaND8w,5338
 aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py,sha256=zhmsRp-8vjB5rRekqTA07d3yb-42HWqng9dDMkvK6hM,623
@@ -121,17 +124,20 @@ aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py,sha256=te06QMF
 aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py,sha256=mDSBOxopDfNhEJeU8fVI8b5lXTYrRzcc97aLbFgYSy4,4413
 aiagents4pharma/talk2knowledgegraphs/utils/__init__.py,sha256=cZqb3LZLmBnmyAtWFv2Z-4uJvQmx0M4zKsfiWrlM3Pk,195
 aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py,sha256=6vQnPkeOWae_8jePjhma3sJuMTngy0I0tqzdFt6OqKg,2507
-aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py,sha256=IlrdGbRGD0IM7eMcpkOjuRjKNuH3lz_X8zN6RHwk61c,1340
+aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py,sha256=8cve_KLtQUhG3uMKYpyelZvpETSsNGRdGE4X0NXMk4M,2442
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py,sha256=POSDrSdFAWsBCueOPD-Fok-ARdTywJU1ivwpT9EU1Kw,199
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py,sha256=1nGznrAj-xT0xuSMBGz2dOujJ7M_IwSR84njxtxsy9A,2523
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_elf6EgzfagFAO5QnL3a_aXZyN7B1EBziu44MTfM,3806
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/nim_molmim.py,sha256=XH6JNfmMS38UEU7UGJeeabHfRykharnQpQaqjO86OlQ,1537
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/ollama.py,sha256=8w0sjt3Ex5YJ_XvpKl9UbhdTiiaoMIarbPUxLBU-1Uw,2378
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
-aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=JKGavA-umsGX3ng17_UYAvDBdbg-W-mPn8Q6JfP7J9U,143
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=K157MWJ4dn2fj3G5ClhyAOXg9jI2H02GP07J6UpasJw,230
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
-aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256=qsVlDCGGDkUCv-R5_xFGhrtLS7P0CfagnM2qATwiOFM,1333
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py,sha256=xSPP-h2q9fABz6Sd6ZlH9WiyoO8KZeEnPI5n2nJpWL4,2443
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256=CQEGQ6Qsex2T91Vw7zTrclJBbSGGhxeWaVJb8tnURAQ,1691
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py,sha256=I0cD0Fk2Uk27_4jEaIhpoGhoMh_RphY1VtkMnk4dkPg,2011
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py,sha256=z0Jb3tt8VzRjzqI9oVcUvRlPPg6BUdmslfKDIEFE_h8,3013
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=NOZxTklAH1j1ggu97Ib8Xn9LCKudEWt-8dx8w7yxVD8,180
@@ -219,8 +225,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=lyrfpx8NH
 aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9yrBYaDnRe7sR6PrpwR82OBJbA2P_Tc6RbxAbM,2748
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
-aiagents4pharma-1.32.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.32.0.dist-info/METADATA,sha256=o3uHTzLfOPglRJUlK6_vKAuJ0qwKhGt7BeiQHeF4U_o,16043
-aiagents4pharma-1.32.0.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-aiagents4pharma-1.32.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.32.0.dist-info/RECORD,,
+aiagents4pharma-1.34.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.34.0.dist-info/METADATA,sha256=P4bmxMTSkbYdRNmw6mijR5O19PBaYRqqP3SgtFhdtpk,16043
+aiagents4pharma-1.34.0.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+aiagents4pharma-1.34.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.34.0.dist-info/RECORD,,