3399 Systematically Integrating Microbiomes and Exposomes for Translational Research
OBJECTIVES/SPECIFIC AIMS: Characterize microbiome metadata describing specimens collected, genomic pipelines and microbiome results, and incorporate them into a data integration platform for enabling harmonization, integration and assimilation of microbial genomics with exposures as spatiotemporal e...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Cambridge University Press
2019-03-01
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| Series: | Journal of Clinical and Translational Science |
| Online Access: | https://www.cambridge.org/core/product/identifier/S2059866119000712/type/journal_article |
| _version_ | 1811156667863138304 |
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| author | Ram Gouripeddi Andrew Miller Karen Eilbeck Katherine Sward Julio C. Facelli |
| author_facet | Ram Gouripeddi Andrew Miller Karen Eilbeck Katherine Sward Julio C. Facelli |
| author_sort | Ram Gouripeddi |
| collection | DOAJ |
| description | OBJECTIVES/SPECIFIC AIMS: Characterize microbiome metadata describing specimens collected, genomic pipelines and microbiome results, and incorporate them into a data integration platform for enabling harmonization, integration and assimilation of microbial genomics with exposures as spatiotemporal events. METHODS/STUDY POPULATION: We followed similar methods utilized in previous efforts in charactering and developing metadata models for describing microbiome metadata. Due to the heterogeneity in microbiome and exposome data, we aligned them along a conceptual representation of different data used in translational research; microbiomes being biospecimen-derived, and exposomes being a combination of sensor measurements, surveys and computationally modelled data. We performed a review of literature describing microbiome data, metadata, and semantics [4–15], along with existing datasets [16] and developed an initial metadata model. We reviewed the model with microbiome domain experts for its accuracy and completeness, and with translational researchers for its utility in different studies, and iteratively refined it. We then incorporated the logical model into OpenFurther’s metadata repository MDR [17,18] for harmonization of different microbiome datasets, as well as integration and assimilation of microbiome-exposome events utilizing the UPIE. RESULTS/ANTICIPATED RESULTS: Our model for describing the microbiome currently includes three domains (1) the specimen collected for analysis, (2) the microbial genomics pipelines, and (3) details of the microbiome genomics. For (1), we utilized biospecimen data model that harmonizes the data structures of caTissue, OpenSpecimen and other commonly available specimen management platform. (3) includes details about the organisms, isolate, host specifics, sequencing methodology, genomic sequences and annotations, microbiome phenotype, genomic data and storage, genomic copies and associated times stamps. We then incorporated this logical model into the MDR as assets and associations that UPIE utilizes to harmonize different microbiome datasets, followed by integration and assimilation of microbiome-exposome events. Details of (2) are ongoing. DISCUSSION/SIGNIFICANCE OF IMPACT: The role of the microbiome and co-influences from environmental exposures in etio-pathology of various pulmonary conditions isn’t well understood [19–24]. This metadata model for the microbiome provides a systematic approach for integrating microbial genomics with sensor-based environmental and physiological data, and clinical data that are present in varying spatial and temporal granularities and require complex methods for integration, assimilation and analysis. Incorporation of this microbiome model will advance the performance of sensor-based exposure studies of the (UPIE) to support novel research paradigms that will improve our understanding of the role of microbiome in promoting and preventing airway inflammation by performing a range of hypothesis-driven microbiome-exposome pediatric asthma studies across the translational spectrum. |
| first_indexed | 2024-04-10T04:55:09Z |
| format | Article |
| id | doaj.art-ccbd34568d0e411f8fe3b7a2a1b527d2 |
| institution | Directory Open Access Journal |
| issn | 2059-8661 |
| language | English |
| last_indexed | 2024-04-10T04:55:09Z |
| publishDate | 2019-03-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Journal of Clinical and Translational Science |
| spelling | doaj.art-ccbd34568d0e411f8fe3b7a2a1b527d22023-03-09T12:30:29ZengCambridge University PressJournal of Clinical and Translational Science2059-86612019-03-013293010.1017/cts.2019.713399 Systematically Integrating Microbiomes and Exposomes for Translational ResearchRam Gouripeddi0Andrew Miller1Karen Eilbeck2Katherine Sward3Julio C. Facelli4The University of Utah School of MedicineUniversity of Utah; University of Utah; The University of Utah School of MedicineUniversity of Utah; University of Utah; The University of Utah School of MedicineUniversity of Utah; University of Utah; The University of Utah School of MedicineThe University of Utah School of MedicineOBJECTIVES/SPECIFIC AIMS: Characterize microbiome metadata describing specimens collected, genomic pipelines and microbiome results, and incorporate them into a data integration platform for enabling harmonization, integration and assimilation of microbial genomics with exposures as spatiotemporal events. METHODS/STUDY POPULATION: We followed similar methods utilized in previous efforts in charactering and developing metadata models for describing microbiome metadata. Due to the heterogeneity in microbiome and exposome data, we aligned them along a conceptual representation of different data used in translational research; microbiomes being biospecimen-derived, and exposomes being a combination of sensor measurements, surveys and computationally modelled data. We performed a review of literature describing microbiome data, metadata, and semantics [4–15], along with existing datasets [16] and developed an initial metadata model. We reviewed the model with microbiome domain experts for its accuracy and completeness, and with translational researchers for its utility in different studies, and iteratively refined it. We then incorporated the logical model into OpenFurther’s metadata repository MDR [17,18] for harmonization of different microbiome datasets, as well as integration and assimilation of microbiome-exposome events utilizing the UPIE. RESULTS/ANTICIPATED RESULTS: Our model for describing the microbiome currently includes three domains (1) the specimen collected for analysis, (2) the microbial genomics pipelines, and (3) details of the microbiome genomics. For (1), we utilized biospecimen data model that harmonizes the data structures of caTissue, OpenSpecimen and other commonly available specimen management platform. (3) includes details about the organisms, isolate, host specifics, sequencing methodology, genomic sequences and annotations, microbiome phenotype, genomic data and storage, genomic copies and associated times stamps. We then incorporated this logical model into the MDR as assets and associations that UPIE utilizes to harmonize different microbiome datasets, followed by integration and assimilation of microbiome-exposome events. Details of (2) are ongoing. DISCUSSION/SIGNIFICANCE OF IMPACT: The role of the microbiome and co-influences from environmental exposures in etio-pathology of various pulmonary conditions isn’t well understood [19–24]. This metadata model for the microbiome provides a systematic approach for integrating microbial genomics with sensor-based environmental and physiological data, and clinical data that are present in varying spatial and temporal granularities and require complex methods for integration, assimilation and analysis. Incorporation of this microbiome model will advance the performance of sensor-based exposure studies of the (UPIE) to support novel research paradigms that will improve our understanding of the role of microbiome in promoting and preventing airway inflammation by performing a range of hypothesis-driven microbiome-exposome pediatric asthma studies across the translational spectrum.https://www.cambridge.org/core/product/identifier/S2059866119000712/type/journal_article |
| spellingShingle | Ram Gouripeddi Andrew Miller Karen Eilbeck Katherine Sward Julio C. Facelli 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research Journal of Clinical and Translational Science |
| title | 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research |
| title_full | 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research |
| title_fullStr | 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research |
| title_full_unstemmed | 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research |
| title_short | 3399 Systematically Integrating Microbiomes and Exposomes for Translational Research |
| title_sort | 3399 systematically integrating microbiomes and exposomes for translational research |
| url | https://www.cambridge.org/core/product/identifier/S2059866119000712/type/journal_article |
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