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Exposures Provider

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Gaurav Vaidya edited this page Dec 13, 2023 · 53 revisions

Team Introduction Page Overview For Exposures Provider

Team Description

The Exposures Provider team created and maintains two KPs: ICEES+ KP and CAM/AOP KP.

ICEES (Integrated Clinical and Environmental Exposures Service) provides open access to clinical data (e.g., EHR data, study data) that have been integrated at the patient level with a variety of environmental exposures data. ICEES thus equips Translator with an open-source model and software code to support gene x environment analysis in the context of real-world health outcomes and observations. ICEES was developed to support specific use cases on asthma and related common pulmonary disorders, primary ciliary dyskinesia and related rare pulmonary disorders, drug-induced liver injury, rare disease phenotypes, and coronavirus infection. However, the general model and associated open-source software code are generalizable to any use case or disease in which integrated clinical and environmental exposures data are valuable. ICEES is being developed in collaboration with investigators affiliated with the Environmental Polymorphisms Registry at the National Institute of Environmental Health Sciences, the UNC Primary Ciliary Dyskinesia Registry, and the international DILI Network.

CAMs (Causal Activity Models) are small knowledge graphs built using the Web Ontology Language (OWL). The CAM database combines multiple CAM graphs with a large merged bio-ontology containing the full vocabulary of concepts referenced within the individual CAMs. Each CAM describes an instantiation of some of those concepts within a particular context, with the interactions between those instances modeled as an interlinked representation of a complex biological or environmental process. Much of the available data are models of biological pathways within cells, having been imported from the Gene Ontology GO-CAM annotation dataset and also through the automated translation of the Reactome pathway knowledgebase into GO-CAM. However, the relation vocabulary and inference systems in the ontology-based implementation are generic and can accommodate many other knowledge domains. Indeed, we are exploring approaches to represent Adverse Outcome Pathways (AOPs) as CAMs. As such, the CAM/AOP KP equips Translator with a flexible tool and open-source software code to expose causal relationships between biological entities chained together to model complex biological and environmental processes.

Team Members

Principal Investigators

  • Stan Ahalt
  • Ashok Krishnamurthy

Core Scientific and Technical Team Members

  • Jim Balhoff - CAM/AOP technical lead; contact with questions
  • Stephen Edwards - CAM/AOP
  • Kara Fecho - ICEES translational science lead; contact with questions
  • Meisha Mandal - CAM/AOP
  • Kenny Morton - ICEES technical advisor, SRI liaison
  • Emily Pfaff - ICEES, clinical informatics advisor
  • Guarav Vaidya - CAM/AOP
  • Max Wang - ICEES technical co-lead
  • Hong Yi - ICEES technical co-lead; contact with questions

Subject Matter Experts

  • David Peden
  • Michael Knowles
  • Margaret Leigh
  • Shepherd Schurman
  • Paul Watkins

Statistical Consultant

  • Perry Haaland

Project Manager

  • Carrie Pasfield

Team Tools

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Knowledge Providers (KP)

Autonomous Relay Agents (ARA)

Autonomous Relay System (ARS)

Standards and Reference Implementation (SRI)

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