Data Services for Geochemical Data
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The document discusses the evolution and services of geological data platforms, particularly EarthChem and its role in the standardized publication and preservation of geochemical data. It highlights the need for community collaboration and best practices to improve data accessibility and integration in geochemical research. Additionally, it outlines the goals of OneGeochemistry to create a global network for fair and interoperable geochemical data sharing.
Data Services for Geochemical Data
- 1. Data Services for Geochemical Data Kerstin Lehnert Lamont-Doherty Earth Observatory, Columbia University Director IEDA/EarthChem/SESAR President IGSN e.V. 1
- 2. Topics ● Geochemical Data Services: EarthChem, Astromat, & SESAR ○ Purpose, services, usage ○ Data structure, metadata content, data exchange ○ Community input and adoption ● OneGeochemistry ○ Why we need it ○ How we can do it AGN Mini-Workshop, March 25, 2020 2
- 3. Overview ● EarthChem: NSF funded AGN Mini-Workshop, March 25, 2020 3
- 4. EarthChem Evolution ● 1996 - 2010: Multiple NSF awards to develop and operate the PetDB database ● 2004 – 2009: NSF awards to develop and operate SESAR & the IGSN ● 2003: EarthChem formed as an alliance of PetDB, NAVDAT, & GEOROC (R. Carlson, A. Hofmann, D. Walker, K. Lehnert) ● 2006 – 2011: NSF award to develop EarthChem as a global one-stop-shop for geochemical data (EarthChem Portal) and infrastructure for community contributions ● 2007 – 2009: Editors Roundtable to develop & promote Best Practices for geochemical data ● 2010 – 2020: EarthChem & SESAR operated & maintained as part of the IEDA Cooperative Agreement with NSF ● 2010: Release of the EarthChem Library (data repository) ● 2016: Inclusion of experimental petrology data systems LEPR and TraceDs AGN Mini-Workshop, March 25, 2020 4
- 5. Geochemical Data Services Data Publication & Preservation Data Mining & Analysis Global Data Network Repository (ECL, Geochron, AstroRep) Synthesis (PetDB, AstroDB, LEPR/TraceDs) Portal (EarthChem Portal) Best Practices Data Standards System development, administration, & operation Review & curation of user submitted data Aggregation & ingestion of published data Community engagement (workshops, newsletter, etc.) Participation in & leadership of national & international initiatives for research data management 5
- 6. EarthChem Architecture & Data Flow 6 EarthChem Synthesis Data, citation, sample metadata method metadata EarthChem Portal Data, citation, sample metadata method metadata NAVDAT GEOROC USGS Geochron Sample metadata & ages Analytical metadata Analytical metadata EarthChem Library Title, authors, keywords, license, etc. Data file & metadata Data file & metadata Lab instruments, manual upload User submission Data ingestion by curators XML data transfer
- 7. EarthChem Library Astromat Repo ● Scope: Publication & archiving of geochemical, petrological, mineralogical, and geochronological data (user contributed) ● Purpose: Support researchers in making their data FAIR ● Content: User submitted datasets (new data, compilations) ● Services: Data curation following international best practices ○ Guidelines & templates for users to document data provenance & quality ○ Web-based data submission & data search/access ○ Dataset review by dedicated curators ○ DOI registration (DataCite) ○ Long-term archiving in Amazon Glacier ○ Links data to publications, samples, funding awards, authors; interoperability with data portals (e.g. DataONE), schema.org ● Structure: File-based system with metadata catalog Repository AGN Mini-Workshop, March 25, 2020 7
- 8. EarthChem’s Best Practices for Geochemical Data ● Following recommendations by the Editors Roundtable, developed between 2007 and 2009 and signed by publishers and data facilities (the precursor to COPDESS). ● Fairly high-level guideline for data reporting, including provenance metadata of analytical measurements, sample identification, and sample metadata. ● EarthChem data submission templates are designed following this guideline. ● Not comprehensive. ● Not a technical standard. AGN Mini-Workshop, March 25, 2020 8 Goldstein, Steven L.; Hofmann, Albrecht W.; Lehnert, Kerstin A. (2014): Requirements for the Publication of Geochemical Data. Interdisciplinary Earth Data Alliance (IEDA). http://dx.doi.org/10.1594/IEDA/100426.
- 9. AGN Mini-Workshop, March 25, 2020 9
- 10. EarthChem Library Usage ● Accepting wide range of data types ○ Observational data, mainly sample-based ■ Chemical & physical properties of different materials (rock, soil, fluid, gas, mineral, etc.) ■ Sample descriptions ○ Data compilations ○ (Method descriptions) ● Not ready for models & software Implementation of FAIR Data policy at AGU/WileyAGN Mini-Workshop, March 25, 2020 10
- 13. Recent ECL Datasets ● Major, trace element and Sr-Nd-Pb isotope data for lavas from Holes 559 and 561 of DSDP Leg 82 ● Magmatism at the Southern End of the East African Rift System: Origin and Role During Early Stage Melting ● Susquehanna Shale Hills Critical Zone Observatory - Cole Farm groundwater surface water chemistry 2018 ● Major and minor element data and mineralogical composition of products from kinetic dolomitization laboratory experiments ● Major and trace element geochemistry of igneous and sedimentary rocks from Lingshan Island, China ● Humic acids and soil organic matter in three forest types in Taiwan ● U-Pb detrital zircon geochronology of the Bagua Basin, Northern Peru ● The emissions of CO2 and other volatiles from the world’s subaerial volcanoes ● Open apatite Sr isotopic system in low-temperature hydrous regimes (Baogutu porphyry Cu deposit, Western Junggar, China) ● Geochemical analyses of ice cores to investigate the hydrology and biogeochemistry of Lake Eggers, McMurdo Sound, Antarctica ● Incubation experiment to investigate the effect of phosphorus slag on the physical-chemical properties of cadmium contaminated soil ● Hafnium isotopes in Eastern North American tholeiites of the Central Atlantic Magmatic Province ● Elemental concentration of carbon and nitrogen in peat from Molokai, Hawaii ● Volatile and major elements in mid-ocean ridge basalt glasses from the Gulf of Aden ● Susquehanna Shale Hills Critical Zone Observatory - Cole Farm Geochemistry ● Pliocene Palaeoclimate off Southeastern Africa: Insights from IODP Expedition 361 AGN Mini-Workshop, March 25, 2020 13
- 14. PetDB (ECS) LEPR, TraceDs AstroDB ● Scope: Synthesis of geochemical and petrological data ● Purpose: Advanced data access & mining (access to individual measurements) ● Content: Published data, processed (harmonized) and ingested by data curators ○ Analytical and experimental observations; compositional (geochemistry, mineralogy) ○ Thematic collections ● Services: Interactive search interface for data exploration & retrieval at the granularity of individual samples/experiments & measurements ● Structure: Relational database ● Special Features: Highly successful data infrastructure for geochemistry since late 1990’s (860 citations in the literature) AGN Mini-Workshop, March 25, 2020 14 Synthesis
- 15. Synthesis Databases: Data Model (ODM2) Feature of Interest Sampling Feature Action Result Method Metadata Annotations Annotations Annotations Annotations Annotations AGN Mini-Workshop, March 25, 2020 15 e.g. geological unit, volcano, lava flow e.g. specimen, core (can have hierarchy) e.g. sample preparation, analysis e.g. measured value Horsburgh, J. S. et al., “Observations Data Model 2: A community information model for spatially discrete Earth observations”, Environmental Modelling & Software, volume 79, 55–74, 2016. https://doi.org/10.1016/j.envsoft.2016.01.010
- 16. EarthChem Synthesis: Data Search & Retrieval ● Give me all 87Sr/86Sr and O isotopes for granites from location X and Y ● Give me all REE data for basaltic samples with Nb < 2ppm ● Give me all data for samples with ages between 2 and 2.5 My ● Give me all olivine compositions for samples with Sr & Nd isotopes available AGN Mini-Workshop, March 25, 2020 16 Example Queries
- 17. EarthChem Portal • 22,074 publications • 1,054,738 samples • 30,059,995 analytical values Access to data in a global federation of geochemical databases • PetDB • SedDB • GEOROC (Germany) • USGS • MetPetDB • GANSEKI (Japan) Machine-readable interfaces Interoperability with modeling tools EarthChemXML for data integration AGN Mini-Workshop, March 25, 2020 17
- 18. AGN Mini-Workshop, March 25, 2020 18
- 19. Value & Impact of Data Synthesis 19 ● Minimize time for data wrangling & reuse ● Allow quick exploration & testing of research hypotheses ● Allow real-world data use in the classroom ● Facilitate and inspire new research paradigms ○ Statistical Geochemistry ○ Machine Learning ○ Neural Network Analysis AGN Mini-Workshop, March 25, 2020 Ueki, K., Hino, H., & Kuwatani, T. (2018). Geochemical discrimination and characteristics of magmatic tectonic settings: A machine-learning-based approach. Geochemistry, Geophysics,Geosystems,19, 1327–1347. https://doi.org/10.1029/2017GC007401
- 20. EarthChem-in-a-Box ● Support community contributions to EarthChem Synthesis ● Support local data management, e.g. for projects or in geochemistry labs AGN Mini-Workshop, March 25, 2020 20 Web applications (Admin, Search, Page Database (ODM2 compliant) APIs Joint Metadata Index Web applications (Admin, Search, Page Database (ODM2 compliant) APIs Web applications (Admin, Search, Page Database (ODM2 compliant) APIs Lab 1 Lab 2 Lab 3
- 21. Challenges for Data Synthesis & Federation 21 ● Lack of internationally endorsed data exchange standard for analytical data ○ Difficulty to automate data ingestion. ○ Hinders growth of federation and accessible data collections. ● Architectures becoming unfit for growing volume of data and increasing demand for access to most or all of the data for data analytics. ● Lack of technical infrastructure or resources for a federation of partner systems. ○ Unable to deliver data in encoded form. ○ Unable to modify systems to align with new architecture or data exchange standards (incl. vocabularies). ● Lack of formal agreements or governance of the federation. AGN Mini-Workshop, March 25, 2020
- 22. OneGeochemistry “OneGeochemistry seeks to create a global geochemical data network that facilitates and promotes discovery and access of geochemical data through coordination and collaboration among international geochemical data providers.” AGN Mini- Works hop, March 22 From: Lehnert K, Wyborn L, Bennett V C, Hezel D, McInnes B I A , Plank T, Rubin K (2019): OneGeochemistry: Towards an Interoperable Global Network of FAIR Geochemical Data. Abstract submitted to CODATA 2019 The Model:
- 23. OneGeochemistry Goals ● Develop internationally endorsed best practices for FAIR geochemical data. ○ Define requirements for data documentation (method, samples, data quality, etc.) ● Develop and implement interoperability standards for geochemical data to enable machine-to-machine exchange and integration of geochemical data. ○ Align with modern technology, e.g. semantic web standards. ○ Use, where possible, internationally endorsed vocabularies. ● Develop a governance model for the organization to ensure participation and trust. ● Develop a business model to ensure long-term sustainability. “We must, indeed, all hang together or, most assuredly, we shall all hang separately”. Benjamin FranklinAGN Mini-Workshop, March 25, 2020 23
- 24. Geochemical Data Standards & Best Practices ● What are the requirements for interoperability and reusability of lab analytical data? ○ We need to define Best Practices for researchers reporting the data. ○ We need to define data structures, vocabularies, and protocols for data managers to allow global integration and exchange of data. ● What standards and best practices exist that can be adopted or adapted? ● Which modern protocols do we need to align with? ● What are the best mechanisms to develop, adopt, and govern such data standards? ● How do we advance the necessary culture change in geochemistry toward open data sharing? AGN Mini-Workshop, March 25, 2020 24
- 25. Geochemistry Is Lagging Behind AGN Mini- Works hop, March 25