BioBricks ICE
BioBricks ICE (Integrated Chemical Environment) is an open knowledge graph for cheminformatics and chemical safety data from EPA's CompTox database.
BioBricks ICE (Integrated Chemical Environment) is an open knowledge graph that serves toxicologists, computational chemists, and environmental health researchers by integrating chemical safety and bioassay data from the EPA's NICEATM ICE database. The graph contains 27.4 million triples describing 206,543 chemical entities linked to over 3 million bioassay measurements across 2,063 standardized assays. Core entities include chemical substances (identified via EPA DSSTox IDs), bioassays (BAO ontology), assay measurements, and mechanistic targets with gene and UMLS identifiers. The graph employs established vocabularies including the BioAssay Ontology (BAO), Chemical Information Ontology (CHEMINF), Semanticscience Integrated Ontology (SIO), and Relation Ontology (RO). External linkages to EPA CompTox Dashboard, NCBI Gene, and UMLS enable cross-database queries. Licensed as public domain (CC0-1.0), the graph supports federation with other toxicology and biomedical knowledge graphs.
provenance:
- derivedFrom:
label: NICEATM ICE
uri: https://ice.ntp.niehs.nih.gov/
kind: Database
license:
data:
label: Public Domain
spdx: CC0-1.0
uri: https://ice.ntp.niehs.nih.gov/DATASETDESCRIPTION
note: >
All data in ICE are publicly available with no restrictions on use.
List assays by source from InvitroDB that are found in both ICE and ToxCast
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX CHEMINF: <http://purl.obolibrary.org/obo/CHEMINF_>
PREFIX CAS: <http://identifiers.org/cas/>
PREFIX EDAM: <http://edamontology.org/>
PREFIX dce: <http://purl.org/dc/elements/1.1/>
PREFIX BAO: <http://www.bioassayontology.org/bao#BAO_>
SELECT ?assay
WHERE {
?assay a BAO:0000015 ;
dce:source "InvitroDB" .
}
LIMIT 100
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v1("?assay"):::projected
c2([http://www.bioassayontology.org/bao#BAO_0000015]):::iri
c4(["InvitroDB"]):::literal
v1 --"a"--> c2
v1 --"dc:source"--> c4
List the names of chemical entities and optionally their CAS RN and DSSTOXSID if available
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX CHEMINF: <http://purl.obolibrary.org/obo/CHEMINF_>
PREFIX CAS: <http://identifiers.org/cas/>
PREFIX EDAM: <http://edamontology.org/>
SELECT ?cas ?dsstox ?name
WHERE {
?s a CHEMINF:000000 ;
rdfs:label ?name .
OPTIONAL {
?s EDAM:has_identifier ?dsstox.
?dsstox a CHEMINF:000568. # DSSTOX SID
}
OPTIONAL {
?s EDAM:has_identifier ?cas .
?cas a CHEMINF:000446 . # CAS RN
}
}
LIMIT 200
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v4("?cas"):::projected
v3("?dsstox"):::projected
v2("?name"):::projected
v1("?s")
c5([obo:CHEMINF_000568]):::iri
c6([obo:CHEMINF_000446]):::iri
c2([obo:CHEMINF_000000]):::iri
v1 --"a"--> c2
v1 --"rdfs:label"--> v2
subgraph optional0["(optional)"]
style optional0 fill:#bbf,stroke-dasharray: 5 5;
v1 -."http://edamontology.org/has_identifier".-> v3
v3 --"a"--> c5
end
subgraph optional1["(optional)"]
style optional1 fill:#bbf,stroke-dasharray: 5 5;
v1 -."http://edamontology.org/has_identifier".-> v4
v4 --"a"--> c6
end
| SPARQL Endpoint | https://frink.apps.renci.org/biobricks-ice/sparql |
|---|---|
| Triple Pattern Fragments | https://frink.apps.renci.org/ldf/biobricks-ice |
| Class | Entities |
|---|
| Property | Triples |
|---|