Resources
Table of Contents
Getting Started
Browse the EHS Ontology Resource Catalog, a compilation of organizations, ontologies/terminologies, and tools useful to harmonizing environmental health research.
Past Events
EHLC Virtual Workshop 2023 – Sharing Your Environmental Health Sciences (EHS) Data: Metadata, Standards, and Tools (January 13, 19, and February 1, 2023)
- January 13 - February 1 Recordings
- EHLC Workshop Report (2023) (1MB)
- Data Management and Sharing Resources (99KB)
CANUE – The Canadian Urban Environmental Health Research Consortium (December 16, 2022)
Environmental Health Language Collaborative (EHLC) – Biolink Webinar (October 7, 2022)
EHLC Occupational History Webinar - Best Practices and Tools for Collecting, Coding, and Using Occupational Information
Environmental Health Language Collaborative (EHLC) - Use Case Champions Webinar (April 4, 2022)
Knowledge Bases As a Tool to Understand the Intersection of Genes, Phenotypes, and Environment (December 10, 2021)
Catalyzing Knowledge-driven Discovery in Environmental Health Sciences Through a Harmonized Language (September 9-10, 2021)
A Primer on Using Terminologies, Vocabularies, and Ontologies for Knowledge Organization (July 20, 2021)
- Meeting Agenda (121KB)
- July 20 Recording
The Value of Creating Language and Community in Catalyzing Knowledge-Driven Discovery in Environmental Health Research (June 24, 2021)
- Meeting Agenda (134KB)
- June 24 Recording
Computable Exposures Workshop (September 9 – 10, 2019)
- Meeting Agenda (20KB)
- Thessen AE, Grondin CJ, Kulkarni RD, Brander S, Truong L, Vasilevsky NA, Callahan TJ, Chan LE, Westra B, Willis M, Rothenberg SE, Jarabek AM, Burgoon L, Korrick SA, Haendel MA. (2020). Community approaches for integrating environmental exposures into human models of disease. Environmental Health Perspectives. 128(12): 125002. [Abstract Thessen AE, Grondin CJ, Kulkarni RD, Brander S, Truong L, Vasilevsky NA, Callahan TJ, Chan LE, Westra B, Willis M, Rothenberg SE, Jarabek AM, Burgoon L, Korrick SA, Haendel MA. (2020). Community approaches for integrating environmental exposures into human models of disease. Environmental Health Perspectives. 128(12): 125002.]
Workshop for the Development of a Framework for Environmental Health Science Language (September 15 – 16, 2014)
- Meeting Agenda
- Publications
- Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M. (2016). Laying a community-based foundation for data-driven semantic standards in environmental health sciences. Environmental Health Perspectives. 124: 1136-1140. [Abstract Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M. (2016). Laying a community-based foundation for data-driven semantic standards in environmental health sciences. Environmental Health Perspectives. 124: 1136-1140.]
- September 15 Recording
- September 16 Recording
Recommended Reading
Gain further insights on the value of terminologies to environmental health science research.
Adverse Outcome Pathways and Aggregate Exposure Pathways
- Hines DE, Edwards SE, and Conolly RB (2019). A case study application of the Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) frameworks to facilitate the integration of human health and ecological endpoints for Cumulative Risk Assessment (CRA). Environmental Science & Technology. 52(2): 839-849. [Abstract Hines DE, Edwards SE, and Conolly RB (2019). A case study application of the Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) frameworks to facilitate the integration of human health and ecological endpoints for Cumulative Risk Assessment (CRA). Environmental Science & Technology. 52(2): 839-849.]
- Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, Whelan M. (2014). Adverse Outcome Pathway (AOP) development I: Strategies and principles. Toxicological Sciences. 142(2): 312-320. [Abstract Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, Whelan M. (2014). Adverse Outcome Pathway (AOP) development I: Strategies and principles. Toxicological Sciences. 142(2): 312-320.]
- Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, Whelan M. (2014). Adverse Outcome Pathway (AOP) development II: Best practices. Toxicological Sciences. 142(2): 321-330. [Abstract Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, Whelan M. (2014). Adverse Outcome Pathway (AOP) development II: Best practices. Toxicological Sciences. 142(2): 321-330.]
Environmental Epidemiology
- Burns CJ, LaKind JS, Mattison DR, Alcala CS, Branch F, Castillo J, Clark A, Clougherty JE, Darney SP, Erickson H, Goodman M, Greiner M, Jurek AM, Miller A, Rooney AA, Zidek A. A matrix for bridging the epidemiology and risk assessment gap (2019). Global Epidemiology. 1: 100005. [Abstract Burns CJ, LaKind JS, Mattison DR, Alcala CS, Branch F, Castillo J, Clark A, Clougherty JE, Darney SP, Erickson H, Goodman M, Greiner M, Jurek AM, Miller A, Rooney AA, Zidek A. A matrix for bridging the epidemiology and risk assessment gap (2019). Global Epidemiology. 1: 100005.]
Exposome
- Escher BI, Hackermuller J, Polte T, Scholz S, Aigner A, Altenburger R, Bohme A, Bopp SK, Werner B, Busch W, Chadeau-Hyam M, Covaci A, Eisentrager A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Gunda H, Annika J, Kleinjas J, Nils K, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Muller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schuurmann G, Schwikowski B, Tan Y-M, Trump S, Walter-Rohde S, Wambaugh JF. (2016). From the exposome to mechanistic understanding of chemical-induced adverse effects. Environment International. 99:97-106. [Abstract Escher BI, Hackermuller J, Polte T, Scholz S, Aigner A, Altenburger R, Bohme A, Bopp SK, Werner B, Busch W, Chadeau-Hyam M, Covaci A, Eisentrager A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Gunda H, Annika J, Kleinjas J, Nils K, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Muller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schuurmann G, Schwikowski B, Tan Y-M, Trump S, Walter-Rohde S, Wambaugh JF. (2016). From the exposome to mechanistic understanding of chemical-induced adverse effects. Environment International. 99:97-106.]
- Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ. (2017). Informatics and data analytics to support exposome-based discovery for public health. Annual Review of Public Health. 20(38): 279-294. [Abstract Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ. (2017). Informatics and data analytics to support exposome-based discovery for public health. Annual Review of Public Health. 20(38): 279-294.]
Integrative Platforms
- Davis AP, Grondin CJ, Johnson RJ, Sciaky D, Wiegers J, Wiegers TC, Mattingly CJ. (2021). Comparative Toxicogenomics Database (CTD): Update 2021. Nucleic Acids Research. 49(D1): D1138-D1143. [Abstract Davis AP, Grondin CJ, Johnson RJ, Sciaky D, Wiegers J, Wiegers TC, Mattingly CJ. (2021). Comparative Toxicogenomics Database (CTD): Update 2021. Nucleic Acids Research. 49(D1): D1138-D1143.]
- Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine J, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. 45(D1): D712-D722. [Abstract Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine J, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. 45(D1): D712-D722.]
Ontologies
- Boyles RR, Thessen AE, and Haendel MA. (2019). Ontology-based data integration for advancing toxicological knowledge. Current Opinion in Toxicology. 16: 67-74. [Abstract Boyles RR, Thessen AE, and Haendel MA. (2019). Ontology-based data integration for advancing toxicological knowledge. Current Opinion in Toxicology. 16: 67-74.]
- Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C. (2012). A toxicology ontology roadmap. ALTEX. 29(20): 129-37. [Abstract Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C. (2012). A toxicology ontology roadmap. ALTEX. 29(20): 129-37.]
- Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. (2014). The Human Phenotype Ontology project: Linking molecular biology and disease through phenotype data. Nucleic Acids Research. 42(D1): D966-D974. [Abstract Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. (2014). The Human Phenotype Ontology project: Linking molecular biology and disease through phenotype data. Nucleic Acids Research. 42(D1): D966-D974.]
- Mattingly CJ, McKone TE, Callahan MA, Blake JA, Cohen Hubai, EA. (2012). Providing the missing link: The Exposure Science Ontology ExO. Environmental Science & Technology. 46(6): 3046-3053. [Abstract Mattingly CJ, McKone TE, Callahan MA, Blake JA, Cohen Hubai, EA. (2012). Providing the missing link: The Exposure Science Ontology ExO. Environmental Science & Technology. 46(6): 3046-3053.]
- Price P and Leonard J. (2019). A proposal for creating a taxonomy of chemical interactions using concepts from the aggregate exposure and adverse outcome pathways. Current Opinion in Toxicology. 16 (Aug): 58-66. [Abstract Price P and Leonard J. (2019). A proposal for creating a taxonomy of chemical interactions using concepts from the aggregate exposure and adverse outcome pathways. Current Opinion in Toxicology. 16 (Aug): 58-66.]
- Whaley P, Edwards SW, Kraft A, Nyhan K, Shapiro A, Watford Sm Wattam S, Wolfe T, Angrish M. (2020). Knowledge organization systems for systematic chemical assessments. Environmental Health Perspectives. [Abstract Whaley P, Edwards SW, Kraft A, Nyhan K, Shapiro A, Watford Sm Wattam S, Wolfe T, Angrish M. (2020). Knowledge organization systems for systematic chemical assessments. Environmental Health Perspectives.]
Recommended Viewing
These recordings are from other events related to the development and/or application of a harmonized language.
Contact
Please submit any resources you would like to see added to Stephanie Holmgren, Office of Data Science.to Top