ICEES (Integrated Clinical and Environmental Exposures Service)¶
Source Information¶
InfoRes ID: infores:icees-kg
Description: ICEES KG is the KG version of the Integrated Clinical and Environmental Exposures Service (ICEES), which provides regulatory-compliant open access to clinical data (e.g., electronic health records, survey data, clinical research data) that have been integrated at the patient level with environmental exposures data (e.g., airborne pollutants, landfills, concentrated animal feeding operations, socio-economic indicators).
Data Access Locations: - https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/ - Automat ICEES Plater loaded KGX jsonl files, plus meta_knowledge_graph.json
Data Provision Mechanisms: f, i, l, e, _, d, o, w, n, l, o, a, d
Data Formats: k, g, x
Data Versioning and Releases: Static dataset released 8-20-2024
Ingest Information¶
Ingest Categories: aggregation_interpreter
Utility: The impact of environmental exposures on clinical status is well known. This knowledge resource aggregates such data from significant institutional expertise within Translator.
Scope: Clinical correlations to environmental exposures.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| nodes.jsonl.gz | https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024 | KGX jsonl file of KGX 'nodes' data from Phase 2 ICEES clinical knowledge provider activities. |
| edges.jsonl.gz | https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024 | KGX jsonl file of KGX 'edges' data from Phase 2 ICEES clinical knowledge provider activities. |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| nodes.jsonl | all | id, name, category, equivalent_identifiers |
| edges.jsonl | all | id, subject, predicate, object, primary_knowledge_source, attributes |
Target Information¶
Target InfoRes ID: infores:icees-kg
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:Disease, biolink:EnvironmentalExposure, biolink:ClinicalIntervention, biolink:PopulationOfIndividualOrganisms, biolink:PhysiologicalProcess, biolink:ComplexMolecularMixture, biolink:SequenceVariant, biolink:SmallMolecule, biolink:Protein, biolink:MolecularMixture, biolink:PhenotypicFeature, biolink:Drug, biolink:GrossAnatomicalStructure" | biolink:Disease, biolink:EnvironmentalExposure, biolink:ClinicalIntervention, biolink:PopulationOfIndividualOrganisms, biolink:PhysiologicalProcess, biolink:ComplexMolecularMixture, biolink:SequenceVariant, biolink:SmallMolecule, biolink:Protein, biolink:MolecularMixture, biolink:PhenotypicFeature, biolink:Drug, biolink:GrossAnatomicalStructure" | k, n, o, w, l, e, d, g, e, _, a, s, s, e, r, t, i, o, n | n, o, t, _, p, r, o, v, i, d, e, d |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:SmallMolecule | UMLS, CHEBI, PUBCHEM.COMPOUND, UNII | |
| biolink:ChemicalExposure | UMLS, CHEBI, PUBCHEM.COMPOUND, UNII | |
| biolink:Drug | UMLS, CHEBI, PUBCHEM.COMPOUND, UNII | |
| biolink:Disease | MONDO, UMLS, NCIT, EFO, UBERON, HP | |
| biolink:InformationContentEntity | UMLS | |
| biolink:PhysiologicalProcess | UMLS | |
| biolink:ComplexMolecularMixture | UMLS | |
| biolink:EnvironmentalExposure | UMLS, PUBCHEM.COMPOUND, NCIT | |
| biolink:PhenotypicFeature | MONDO, UMLS, EFO, NCIT, CHEBI, UBERON, NCBIGene, MESH, NCBITaxon, HP | |
| biolink:Activity | UMLS | |
| biolink:PopulationOfIndividualOrganisms | UMLS | |
| biolink:PhysicalEntity | UMLS | |
| biolink:GrossAnatomicalStructure | UBERON | |
| biolink:OrganismAttribute | UMLS | |
| biolink:ChemicalEntity | MESH, UMLS, CHEBI, NCIT | |
| biolink:Device | UMLS | |
| biolink:Phenomenon | UMLS | |
| biolink:Procedure | UMLS | |
| biolink:MolecularMixture | PUBCHEM.COMPOUND | |
| biolink:SequenceVariant | MESH, UMLS, NCBIGene | |
| biolink:Protein | UMLS, NCBIGene | |
| biolink:Gene | NCBIGene | |
| biolink:OrganismTaxon | NCBITaxon, UMLS | |
| biolink:ClinicalIntervention | UMLS |
Future Modeling Considerations¶
None: None
Additional Notes: None
Provenance Information¶
Contributors: - Richard Bruskiewich - data modeling, code author" - {'Evan Morris': 'code support"'} - {'Sierra Moxon': 'data modeling, code support"'} - Matthew Brush - data modeling, domain expertise"
Artifacts: - None