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Milestone - Harmonizing environmental science standards support linking of climate data (2.9) #502

Open ssarrafan opened 1 year ago

ssarrafan commented 1 year ago

Environmental science standards to support linking with microbiome data While there are many existing challenges to fully leverage microbiome data for climate science (11), a tangible, near-term challenge that can be addressed is the need to support linked data standards for relevant environmental processes, environmental variables, and environment types. Similar challenges have been addressed for genomic medicine applications where gene and health outcome data standards were modeled (e.g., Fast Healthcare Interoperability Resources (15) and Observational Medical Outcomes Partnership (16)) and standardized vocabularies such as Systematized Nomenclature of Medical Terms (17)) were developed. To study the association between microscale processes all the way to the ecosystem scale, it is essential to compare variables across studies through meta-analyses which is only possible through standardizing data. Thus, we aim to catalyze interoperable ‘planetary health records’ through the creation of metadata crosswalks between all elements in the NMDC schema and multiple different environmental standards (Milestone 2.9).

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ssarrafan commented 3 months ago

@cmungall this is due this quarter. Any update? Will this be done by September?

ssarrafan commented 3 months ago

Discussed with Emiley and Alicia today. Emiley would like to discuss this milestone with @shreddd to determine if we should focus on this milestone.

ssarrafan commented 1 month ago

@emileyfadrosh @shreddd did you discuss this milestone? @sierra-moxon anything I can add for this DOE report for this milestone?

sierra-moxon commented 1 month ago

There have been several pull requests initiated and merged in the environmental ontology repo including term fixes to harmonize with GOLD: https://github.com/EnvironmentOntology/envo/pull/1517 https://github.com/EnvironmentOntology/envo/pull/1519 - new release of ENVO ecoregion updates: https://github.com/EnvironmentOntology/envo/pull/1523, https://github.com/EnvironmentOntology/envo/pull/1526 animal constructs: https://github.com/EnvironmentOntology/envo/pull/1530 bioremediation: https://github.com/EnvironmentOntology/envo/pull/1534 I think these all relate to the larger milestone of harmonizing environmental standards

sierra-moxon commented 1 month ago

The work from the ENV triad group has also identified several issues with ENVO broad, medium, and local scale terms, currently documented in a set of summary spreadsheets, mostly centering around identifying and reconciling the axis of differentiation in these terms sets. We expect ENVO changes to come out of this effort as well as a constrained set of terms for each environment/module. In addition we are working steadily towards a set of reusable scripts that help us identify and extract ENVO subsets to use in constraining the submission portal and field notes application to help users choose terms. Finally, we have proposed and are working on a generic ontology loader into NMDC as well as a node normalizer so that user-entry into our system is more robust (they can have access to definitions, synonyms, cross references, and more with the ENV triad terms). This will help users pick consistent terms to define their samples. This will help harmonize the samples across our data sets.

sierra-moxon commented 1 month ago

I do not believe this is completed, and should be an ongoing milestone (as I understand it)