MCP Server Proto-OKN

# Chemical Compound Identifiers in Knowledge Graphs - Chat Transcript ## Finding Knowledge Graphs with Chemical Compound Information 👤 **User** Find KGs that have information about chemical compounds, in particular look for common chemical identifiers. Create a table with the KG name, the URI, and the type of chemical identifier. --- 🧠 **Assistant** I'll search through the available knowledge graphs to find ones that contain information about chemical compounds and their identifiers. After examining multiple knowledge graphs, I found several that contain chemical compound information: | KG Name | URI | Chemical Identifiers | |---------|-----|---------------------| | **BioBricks ICE** | https://frink.apps.renci.org/biobricks-ice/sparql | **EPA DSSTox ID (DTXSID)**, UMLS Concept IDs, Entrez Gene IDs (for targets) | | **BioBricks ToxCast** | https://frink.apps.renci.org/biobricks-toxcast/sparql | **EPA DSSTox ID (DTXSID)**, **InChIKey** | | **BioBricks Tox21** | https://frink.apps.renci.org/biobricks-tox21/sparql | **CAS Registry Number** (via identifiers.org URIs) | | **BioBricks PubChem Annotations** | https://frink.apps.renci.org/biobricks-pubchem-annotations/sparql | **PubChem Compound ID (CID)**, InChI, InChIKey, SMILES, Molecular Formula, Chemical Names | | **BioBricks AOP-Wiki** | https://frink.apps.renci.org/biobricks-aopwiki/sparql | **CAS Registry Number**, **InChI**, **InChIKey**, **PubChem Compound ID**, **ChEBI ID**, **SMILES** (with cross-references to ChEMBL, KEGG, Wikidata) | | **BioBricks MeSH** | https://frink.apps.renci.org/biobricks-mesh/sparql | MeSH Descriptor IDs for chemicals (Category D - Chemicals and Drugs), Supplementary Concept Records for specific substances | **Key Chemical Identifier Types Found:** 1. **EPA DSSTox ID (DTXSID)** - EPA's standardized identifier for toxicity testing 2. **CAS Registry Number** - Chemical Abstracts Service registry numbers 3. **InChI/InChIKey** - International Chemical Identifier (textual and hashed versions) 4. **PubChem Compound ID (CID)** - NCBI PubChem database identifiers 5. **ChEBI ID** - Chemical Entities of Biological Interest identifiers 6. **SMILES** - Simplified Molecular Input Line Entry System 7. **MeSH Descriptors** - Medical Subject Headings for chemicals 8. **Molecular Formula** - Chemical formula notation The BioBricks suite provides the most comprehensive chemical coverage, with ICE, ToxCast, and Tox21 focusing on toxicology data, PubChem Annotations providing broader chemical information, and AOP-Wiki connecting chemicals to adverse outcome pathways with extensive cross-referencing. --- ## Adding SPOKE-OKN and SAWGraph 👤 **User** @spoke-okn, @sawgraph have chemical entities. Add them to the table --- 🧠 **Assistant** After examining SPOKE-OKN and SAWGraph knowledge graphs, here's the updated comprehensive table: | KG Name | URI | Chemical Identifiers | |---------|-----|---------------------| | **BioBricks ICE** | https://frink.apps.renci.org/biobricks-ice/sparql | **EPA DSSTox ID (DTXSID)**, UMLS Concept IDs, Entrez Gene IDs (for targets) | | **BioBricks ToxCast** | https://frink.apps.renci.org/biobricks-toxcast/sparql | **EPA DSSTox ID (DTXSID)**, **InChIKey** | | **BioBricks Tox21** | https://frink.apps.renci.org/biobricks-tox21/sparql | **CAS Registry Number** (via identifiers.org URIs) | | **BioBricks PubChem Annotations** | https://frink.apps.renci.org/biobricks-pubchem-annotations/sparql | **PubChem Compound ID (CID)**, InChI, InChIKey, SMILES, Molecular Formula, Chemical Names | | **BioBricks AOP-Wiki** | https://frink.apps.renci.org/biobricks-aopwiki/sparql | **CAS Registry Number**, **InChI**, **InChIKey**, **PubChem Compound ID**, **ChEBI ID**, **SMILES** (with cross-references to ChEMBL, KEGG, Wikidata) | | **BioBricks MeSH** | https://frink.apps.renci.org/biobricks-mesh/sparql | MeSH Descriptor IDs for chemicals (Category D - Chemicals and Drugs), Supplementary Concept Records for specific substances | | **SPOKE-OKN** | https://frink.apps.renci.org/spoke-okn/sparql | **ChEMBL Compound ID**, **ChEBI ID**, **DrugBank ID**, **SMILES** (standardized and regular), Synonyms | | **SAWGraph** | https://frink.apps.renci.org/sawgraph/sparql | **CAS Registry Number**, Substance IDs (internal), PFAS-specific compound identifiers | **Key Chemical Identifier Types Found:** 1. **EPA DSSTox ID (DTXSID)** - EPA's standardized identifier for toxicity testing 2. **CAS Registry Number** - Chemical Abstracts Service registry numbers 3. **InChI/InChIKey** - International Chemical Identifier (textual and hashed versions) 4. **PubChem Compound ID (CID)** - NCBI PubChem database identifiers 5. **ChEBI ID** - Chemical Entities of Biological Interest identifiers 6. **ChEMBL Compound ID** - European Bioinformatics Institute drug database identifiers 7. **DrugBank ID** - Drug and drug target database identifiers 8. **SMILES** - Simplified Molecular Input Line Entry System 9. **MeSH Descriptors** - Medical Subject Headings for chemicals 10. **Molecular Formula** - Chemical formula notation **Notes:** - **SPOKE-OKN** focuses on biomedical compounds including drugs with ChEMBL and DrugBank identifiers - **SAWGraph** specializes in PFAS contamination monitoring with CAS numbers for environmental contaminants - The BioBricks suite provides comprehensive toxicology-focused chemical data - Cross-referencing between KGs is possible via shared identifiers like CAS numbers, ChEBI IDs, and InChI/InChIKeys --- ## Detailed Schema Verification 👤 **User** Check the schemas you retrieved for any compounds or chemical entities or CAS numbers --- 🧠 **Assistant** After detailed examination of the actual data and schemas in each knowledge graph, here's the verified and comprehensive table: | KG Name | URI | Chemical Identifier Types (Verified in Data) | |---------|-----|---------------------------------------------| | **BioBricks ICE** | https://frink.apps.renci.org/biobricks-ice/sparql | **EPA DSSTox ID (DTXSID)** - used as URI in chemical entities<br>CHEMINF classes: Chemical Identifier (000446), Chemical Structure Descriptor (000568), Chemical Information (000000) | | **BioBricks ToxCast** | https://frink.apps.renci.org/biobricks-toxcast/sparql | **EPA DSSTox ID (DTXSID)** - used as URI in chemical structure descriptors<br>**CAS Registry Number** - via identifiers.org/cas URIs<br>CHEMINF classes: Chemical Identifier (000446), Chemical Structure Descriptor (000568) | | **BioBricks Tox21** | https://frink.apps.renci.org/biobricks-tox21/sparql | **CAS Registry Number** - via identifiers.org/cas URIs (primary identifier)<br>CHEMINF class: Chemical Identifier (000446) | | **BioBricks PubChem Annotations** | https://frink.apps.renci.org/biobricks-pubchem-annotations/sparql | **PubChem Compound ID (CID)** - in compound URIs<br>Annotations link to PubChem compounds; specific chemical properties in annotation bodies | | **BioBricks AOP-Wiki** | https://frink.apps.renci.org/biobricks-aopwiki/sparql | *Currently empty/no data available*<br>Schema indicates support for: CAS, InChI, InChIKey, PubChem CID, ChEBI ID, SMILES | | **BioBricks MeSH** | https://frink.apps.renci.org/biobricks-mesh/sparql | **MeSH Descriptor IDs** for chemicals (Category D)<br>**Supplementary Concept Records** for specific chemical substances<br>Tree numbers for hierarchical classification | | **SPOKE-OKN** | https://frink.apps.renci.org/spoke-okn/sparql | **InChIKey** - primary URI format for chemical entities<br>**ChEMBL Compound ID** - via hasDbXref cross-references<br>**DrugBank ID** - via hasDbXref cross-references<br>**PubChem Compound ID** - via hasDbXref<br>**KEGG Compound ID** - via hasDbXref<br>**KEGG Drug ID** - via hasDbXref<br>**BioCyc ID** - via hasDbXref<br>**PDB Ligand ID** - via hasDbXref<br>**SMILES** - as property values (smiles, standardized_smiles) | | **SAWGraph** | https://frink.apps.renci.org/sawgraph/sparql | **CAS Registry Number** - via coso:casNumber property<br>**Substance ID** - via coso:substanceID property<br>Focuses on PFAS compounds and environmental contaminants | **Key Findings:** 1. **CAS Registry Numbers** are used across multiple KGs (ToxCast, Tox21, SAWGraph) as a common identifier 2. **EPA DSSTox IDs (DTXSID)** are the primary identifier in toxicology-focused KGs (ICE, ToxCast) 3. **SPOKE-OKN uses InChIKey as the primary URI** with extensive cross-references to other databases 4. **PubChem Compound IDs** appear in multiple KGs as cross-references 5. **CHEMINF ontology classes** (000446, 000568, 000000) are used in BioBricks toxicology KGs 6. **identifiers.org** is commonly used as a namespace for chemical identifiers 7. **BioBricks AOP-Wiki** endpoint appears to be empty despite having a comprehensive schema **Cross-referencing potential:** CAS numbers, PubChem CIDs, ChEBI IDs, and InChIKeys can enable federation between these knowledge graphs. **Example Data Patterns Found:** **BioBricks ToxCast - CAS Numbers:** ``` http://identifiers.org/cas/100-00-5 http://identifiers.org/cas/100-01-6 ``` **BioBricks ICE - DTXSID:** ``` https://comptox.epa.gov/dashboard/chemical/details/DTXSID80875834 https://comptox.epa.gov/dashboard/chemical/details/DTXSID6064084 ``` **SPOKE-OKN - InChIKey with cross-references:** ``` Subject: http://rdf.ncbi.nlm.nih.gov/pubchem/inchikey/CXOFVDLJLONNDW-UHFFFAOYSA-N Cross-reference: http://identifiers.org/drugbank/DB00252 Cross-reference: http://identifiers.org/chembl.compound/CHEMBL496 Cross-reference: http://identifiers.org/pubchem.compound/3598 ``` **SAWGraph - CAS Numbers for PFAS:** ``` PFHXS: CAS 108427538 PFDS: CAS 126105348 ``` --- 👤 **User** create a transcript --- *Created by [mcp-proto-okn](https://github.com/sbl-sdsc/mcp-proto-okn) on 2025-12-16*