is a Data Source.
CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health.
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infores:ctd
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| ctd.chem_gene_ixns | CTD Chemical-Gene Interactions | CTD_chem_gene_ixns.tsv.gz (41.1 MB) | Product | tsv | Curated chemical-gene and chemical-pr... |
| ctd.chem_gene_ixn_types | CTD Chemical-Gene Interaction Types | CTD_chem_gene_ixn_types.obo (20.7 KB) | Ontology | obo | The hierarchical controlled vocabular... |
| ctd.chemicals_diseases | CTD Chemical-Disease Associations | CTD_chemicals_diseases.tsv.gz (154.4 MB) | Product | tsv | Chemical-disease associations, both c... |
| ctd.chem_go_enriched | CTD Chemical-GO Enriched Associations | CTD_chem_go_enriched.tsv.gz (137.7 MB) | Product | tsv | Gene Ontology terms statistically enr... |
| ctd.chem_pathways_enriched | CTD Chemical-Pathway Enriched Associations | CTD_chem_pathways_enriched.tsv.gz (39.5 MB) | Product | tsv | KEGG and Reactome pathways statistica... |
| ctd.genes_diseases | CTD Gene-Disease Associations | CTD_genes_diseases.tsv.gz (3.0 GB) | Product | tsv | Gene-disease associations, both curat... |
| ctd.genes_pathways | CTD Gene-Pathway Associations | CTD_genes_pathways.tsv.gz (1.0 MB) | Product | tsv | Gene-pathway associations linking NCB... |
| ctd.diseases_pathways | CTD Disease-Pathway Associations | CTD_diseases_pathways.tsv.gz (6.1 MB) | Product | tsv | Disease-pathway associations inferred... |
| ctd.pheno_term_ixns | CTD Chemical-Phenotype Interactions | CTD_pheno_term_ixns.tsv.gz (22.9 MB) | Product | tsv | Curated chemical-phenotype interactio... |
| ctd.exposure_studies | CTD Exposure-Study Associations | CTD_exposure_studies.tsv.gz (562.3 KB) | Product | tsv | Curated exposure studies, one row per... |
| ctd.exposure_events | CTD Exposure-Event Associations | CTD_exposure_events.tsv.gz (4.5 MB) | Product | tsv | Curated exposure events, one row per ... |
| ctd.phenotype_disease_bp | CTD Phenotype-Disease Inference Network (Biological Process) | CTD_Phenotype-Disease_biological_process_associations.tsv.gz (48.0 MB) | Product | tsv | Inferred associations between Gene On... |
| ctd.phenotype_disease_cc | CTD Phenotype-Disease Inference Network (Cellular Component) | CTD_Phenotype-Disease_cellular_component_associations.tsv.gz (3.0 MB) | Product | tsv | Inferred associations between Gene On... |
| ctd.phenotype_disease_mf | CTD Phenotype-Disease Inference Network (Molecular Function) | CTD_Phenotype-Disease_molecular_function_associations.tsv.gz (5.2 MB) | Product | tsv | Inferred associations between Gene On... |
| ctd.chemicals | CTD Chemical Vocabulary | CTD_chemicals.tsv.gz (10.2 MB) | Product | tsv | CTD's hierarchical chemical vocabular... |
| ctd.medic | CTD Disease Vocabulary (MEDIC) | CTD_diseases.obo.gz (1.4 MB) | Ontology | obo | MEDIC, CTD's disease vocabulary, a mo... |
| ctd.anatomy | CTD Anatomy Vocabulary | CTD_anatomy.tsv.gz (317.3 KB) | Product | tsv | CTD's anatomy vocabulary, a modified ... |
| ctd.genes | CTD Gene Vocabulary | CTD_genes.tsv.gz (117.2 MB) | Product | tsv | CTD's gene vocabulary, keyed by NCBI ... |
| ctd.pathways | CTD Pathway Vocabulary | CTD_pathways.tsv.gz (41.6 KB) | Product | tsv | CTD's pathway vocabulary, a list of p... |
| ctd.exposure_ontology | CTD Exposure Ontology (ExO) | CTD_exposure_ontology.obo (59.8 KB) | Ontology | obo | The draft Exposure Ontology (ExO) as ... |
| ctd.batch_query | CTD Batch Query | batchQuery.go | Graphical Interface | http | Web tool for retrieving customized CT... |
| ctd.tetramers | CTD Tetramers | query.go?type=tetramer | Graphical Interface | http | Web query for CTD Tetramers, computat... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| automat.ctd | ctd_automat | f92c663160ec5e36 | Graph | kgx-jsonl | had primary source | CTD Automat |
| bioteque.embeddings | Bioteque Embeddings | embeddings | Product | mixed | had primary source | Network embeddings of the Bioteque gr... |
| mechreponet.kg | MechRepoNet Knowledge Graph | publication | Product | mixed | had primary source | The MechRepoNet knowledge graph in it... |
| kg-monarch.graph | KGX Distribution of KG-Monarch | monarch-kg.tar.gz (220.2 MB) | Graph | kgx | had primary source | KGX Distribution of KG-Monarch |
| kg-monarch.graph.jsonl | KGX JSON-L Distribution of KG-Monarch | monarch-kg.jsonl.tar.gz (301.0 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.rdf | RDF Distribution of KG-Monarch | monarch-kg.nt.gz (838.5 MB) | Graph | rdfxml | had primary source | RDF Distribution of KG-Monarch |
| kg-monarch.graph.neo4j | Neo4j Dump of KG-Monarch | monarch-kg.neo4j.dump (1.3 GB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch |
| kg-monarch.graph.duckdb | DuckDB database of KG-Monarch | monarch-kg.duckdb (6.4 GB) | Graph | mixed | had primary source | DuckDB database of KG-Monarch |
| pheknowlator.graph | PheKnowLator graph | knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator | Graph | owl | had primary source | PheKnowLator graph files, including s... |
| kg-monarch.graph.jsonl.edges | KGX JSON-L Distribution of KG-Monarch Edges | monarch-kg.jsonl.tar.gz (465.3 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.jsonl.nodes | KGX JSON-L Distribution of KG-Monarch Nodes | monarch-kg.jsonl.tar.gz (465.3 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.neo4j.edges | Neo4j Dump of KG-Monarch Edges | monarch-kg_edges.neo4j.csv (4.1 GB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch Edges |
| kg-monarch.graph.neo4j.nodes | Neo4j Dump of KG-Monarch Nodes | monarch-kg_nodes.neo4j.csv (333.4 MB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch Nodes |
| aop-db.data | AOP-DB Data | adverse-outcome-pathway-database-aop-db-version-2 | Product | http | had primary source | The EPA has developed the Adverse Out... |
| ibkh.graph | iBKH Knowledge Graph | ❔ | Graph | mixed | had primary source | The integrative Biomedical Knowledge ... |
| kg-microbe.graph.raw | KG-Microbe KGX Graph - Raw | latest | Graph | kgx | had primary source | Raw source files for all KG-Microbe f... |
| kg-microbe.graph.core | KG-Microbe KGX Graph - Core | latest | Graph | kgx | had primary source | The core KG KG-Microbe-Core with onto... |
| kg-microbe.graph.biomedical | KG-Microbe KGX Graph - Biomedical | latest | Graph | kgx | had primary source | Core plus human biomedical data (onto... |
| kg-microbe.graph.function | KG-Microbe KGX Graph - Function | latest | Graph | kgx | had primary source | Core plus Uniprot genome annotations |
| kg-microbe.graph.biomedical-function | KG-Microbe KGX Graph - Biomedical-Function | KGMicrobe-biomedical-function-20250222.tar.gz (4.3 GB) | Graph | kgx | had primary source | Biomedical plus Uniprot genome annota... |
| cam-kp.ctd-interactions | CTD Chemical-Gene Models | ❔ | Product | http | had primary source | Chemical-gene interaction models and ... |
| translator.ctd.graph | Translator CTD KGX Graph | latest | Graph | kgx-jsonl | had primary source | KGX JSONL graph package for CTD distr... |
| unibiomap.links | UniBioMap Graph Links | unibiomap.links.csv (1.3 GB) | Graph | csv | had primary source | Core UniBioMap graph edges file. |
| unibiomap.auxs | UniBioMap Graph Auxiliaries | unibiomap.auxs.tsv (563.9 MB) | Graph | tsv | had primary source | Auxiliary UniBioMap graph annotations... |
| unibiomap.pred | UniBioMap Predicted Graph | unibiomap.pred.csv (2.3 GB) | Graph | csv | had primary source | Predicted UniBioMap graph edges with ... |
| unibiomap.pred.full | UniBioMap Predicted Graph (Full) | unibiomap.pred.full.csv (5.9 GB) | Graph | csv | had primary source | Full unfiltered UniBioMap predicted g... |
| translator.translator_kg.graph | Translator Aggregate KGX Graph | latest | Graph | kgx-jsonl | had primary source | Aggregated KGX JSONL graph package co... |
| oregano.graph | OREGANO Knowledge Graph | Graphs | Graph | http | was derived from | The OREGANO knowledge graph dataset i... |
| pharmebinet.json | PharMeBINet JSON Release | content (1.8 GB) | Graph | json | was derived from | PharMeBINet V2 JSON release published... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (1.8 GB) | Graph | tsv | was derived from | PharMeBINet V2 TSV release published ... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (1.9 GB) | Graph | mixed | was derived from | PharMeBINet V2 GraphML release publis... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (3.6 GB) | Graph | neo4j | was derived from | PharMeBINet V2 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (3.4 GB) | Graph | neo4j | was derived from | PharMeBINet V2 Neo4j dump release pub... |
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| psygenet.genedisease | PsyGeNET Gene-Disease Associations | www.psygenet.org | Product | tsv | was derived from | Gene-disease associations for psychia... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | Graph | neo4j | was derived from | Neo4j knowledge graph serialization o... |
| pathwaycommons.downloads | Pathway Commons Data Downloads | v14 | Product | mixed | was derived from | Download directory for Pathway Common... |
| pathwaycommons.sif | SIF Network Format | pc-hgnc.sif.gz (9.4 MB) | Product | sif | was derived from | PC v14 Simple Interaction Format netw... |
| pathwaycommons.gmt | GMT Gene Set Format | pc-hgnc.gmt.gz (256.4 KB) | Product | tsv | was derived from | PC v14 Gene Matrix Transposed gene se... |
| pathwaycommons.txt | Extended SIF TXT Format | pc-hgnc.txt.gz (110.3 MB) | Product | txt | was derived from | PC v14 tab-delimited extended SIF nod... |
| biobtree.api | BioBTree REST API | api | Programming Interface | http | had primary source | REST API for searching identifiers an... |
| genecards.web.interface | GeneCards Web Interface | www.genecards.org | Graphical Interface | http | had primary source | Web-based interface for searching and... |
| biobtree.graph.human-subgraph | BioBTree Knowledge Graph - Human Subgraph (KGX) | 20816742 | Graph | kgx | had primary source | Human-scoped, Neo4j-ready subgraph of... |
| kg-alzheimers.graph ⚠ | KGX Distribution of KG-Alzheimers | kg-alzheimers.tar.gz (201.1 MB) | Graph | kgx | had primary source | KGX Distribution of KG-Alzheimers |
| molecular-data-kp.graph.nodes | Nodes for Molecular Data KP | nodes.tsv (3.4 GB) | Graph | kgx | had primary source | KGX nodes for Molecular Data KP |
| molecular-data-kp.graph.edges | Edges for Molecular Data KP | edges.tsv (18.8 GB) | Graph | kgx | had primary source | KGX edges for Molecular Data KP |
| pharmdb.graph | PharmDB-K Graph | ❔ | Graph | http | had primary source | Integrated pharmacological knowledge ... |
| primekg.graph ⚠ | PrimeKG Full Dataset | 6180620 | Graph | csv | had primary source | The full PrimeKG dataset containing d... |
| sri-reference-kg.graph | SRI-Reference KG (KGX distribution) | monarch-kg.tar.gz (219.4 MB) | Graph | kgx | had primary source | KGX distribution of the SRI-Reference KG |
Created: March 09, 2025 | Last modified: September 23, 2026