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EarthChem: Geochemistry Information Network

A community resource that compiles, serves, and visualizes geochemical and geochronological data, with fine-grained access and comprehensive sample metadata.

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EarthChem: Geochemistry Information Network

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  1. EarthChem:Geochemistry Information Network Kerstin Lehnert Registry for Earth samples that administers unique identifiers Steve Goldstein

  2. EarthChem • A community resource that facilitates the compilation, communication, serving, and visualization of geochemical & geochronological data • Based on long-term collaboration of independent data systems for igneous geochemistry: PetDB, GEOROC, & NAVDAT Ocean Islands & Seamounts Oceanic Plateaus Flood Basalts (marine & continental) Convergent Margins Archean Cratons Mid-ocean ridges Back-arc basins Near-axis seamounts Fracture zones Old oceanic crust (Hydrothermal vent fluids & deposits) Volcanic & intrusive of Western North America (Mesozoic and younger)

  3. A New Generation of Integrative Solid Earth Geochemical Databases • Fine-grained access to data: Each individual chemical value is searchable • Comprehensive sample & analytical metadata • Interactive, dynamic interfaces • Allow users to generate customized data sets to view & download • Support for data analysis (system specific) • Data integration • Data visualization, maps, plotting tools

  4. SedDBGeochemical Data for Marine Sediments Development Phase 1 2005-2008 • New data model • Handling of depth domain • tracks relation of samples & sub-samples • Includes age models • Compilation of data sets for 3 test bed areas (Equatorial Pacific, MARGINS SubFac focus areas IBM & CentAm) • Development of data analysis tools (e.g. depth-age conversion, depth-based data integration) ongoing • SedDB vs. 0.1 released Fall 2006 • SedDB vs. 1.0 to be released Summer 2007 (beta version) Current contents: - 77,000 chemical values • 15,350 samples Project Scientists: K. Lehnert (LDEO), S. Goldstein (LDEO), R. Murray (Boston U), N. Pisias (OSU)

  5. Data Types in EarthChem Databases • Geochemical & geochronological data • > 200 chemical parameters : major oxides, trace elements, noble gases, stable & radiogenic isotope ratios • Any material: Whole rock, glass, minerals, melt or fluid inclusions, biogenic components, porewater, leachates, grain size fractions • Published data compiled from the literature and data submitted by investigators • US NSF increasingly enforcing policies for federally funded data to be deposited in public archives

  6. EarthChem Project • Build a central access point for geochemical data (One-Stop-Shop: EarthChem Portal) • Increase availability of data • Build new datasets • Facilitate submission of data by investigators (“Digital Lab Book”) • Facilitate the creation of new datasets by the community • Expand EarthChem database federation • Promote & implement best practices & standards for geochemical data (publication, citation, metadata)

  7. EarthChem Portal • XML schema for data exchange, compatible with GeoSciML (IUGS/CGI) • Portal version 1.0 released in August 2006 • databases export data holdings to XML database at KGS (REST/SOAP web services) • query by location, rock type, reference • works with core databases PetDB, NAVDAT, GEOROC • map interfaces, plotting tools • “Data Citation Index” (to be released June 2007)

  8. Science Program CoreWall CIG MELTS Portals Modeling Tools Visualization Tools GeoMapApp EarthRef Data Integration Tools & Maps Modeling Tools, Synthesis Interoperability - to come Open access to data holdings via XML-based web services

  9. New Datasets • EarthChem Data Compilations • Deep Lithosphere Dataset (xenoliths); status: 45,800 values • Geochronology (under development) • GeoEarthScope • EarthTime • Antarctic rock geochemistry (in planning, collaboration w/ USPRR) • Datasets that will be accessible via the portal • SedDB (Marine sediments) • PaleoStrat (Chemostratigraphic data for terrestrial sedimentary rocks) • MexDB (TransMexican Belt Volcanics, L. Ferrari & S.Straub) • USGS Rock Geochemistry (400,000 samples, mixed lithologies) • MetPetDB - Metamorphic Petrology Database (F. Spear) • Tethys (Ophiolites)

  10. Developing Best Practices • Data Reporting • Completeness of datasets in publications • Standards for analytical technique metadat • Sample metadata, unique identifiers for samples • Citation of data, credit to data authors • “Data Citation Index” • Unique identifiers for data (STD-DOI) • Data management tools for investigators • Access to samples

  11. Problem: Sample Identification • Geochemical samples are analyzed at different times, with different objectives, in different labs • When new methods are developed, they are usually applied to known (previously analyzed) samples • Easy (inevitable) to lose track of a sample’s history

  12. Examples: Ambiguous Naming of Rock Samples Examples from the PetDB Database Sample names are duplicated. Sample names are modified or changed.

  13. Registry that provides & manages unique identifiers for samples • IGSN - International Geo Sample Number • Assigned upon registration of samples (submission of sample metadata) • Catalog & archive of sample metadata • Access to sample metadata via web site & web services • Long-term preservation of metadata • Link to sample archives • Building a Global Sample Catalog • Facilitates links to data • IGSN will be incorporated into persistent resolvable GUIDs (handle.net service at GeoForschungszentrum Potsdam) www.geosamples.org

  14. The International Geo Sample Number IGSN:SIO001324 • Managed at a central registry (SESAR) • Generated by SESAR or by ‘Trusted Agents’ (status granted upon request, strict compliance with the IGSN syntax required) • Does not replace personal or institutional names. • Applied in sample curation, data publication, & digital data management • Nearly 4 Mio. IGSNs assigned so far Unique user code (name space) String of characters

  15. www.geosamples.org

  16. EarthChem System Architecture

  17. Status: Data Submission • Proto-type of data submission tool tested • Uses Microsoft Excel data submission templates. • Java multi-platform tool checks data submission template spreadsheets for errors and submits the data. • The tool makes use of the live production database to fetch constrained lists via web-services. • The code/logic of this tool will be easily transferred into a servlet that will allow submissions via a web-site.

  18. Status: Outreach & Education • Partnerships • Workshops & Short-courses • Exhibits & Demonstrations

  19. PetDB Data Entry Form

  20. Example: PaleoStrat

  21. Questions Data Submission • Data Submission • What is the easiest way to submit data? • What metadata need to be enforced (our demands), what are desired (your demands)? • How can EarthChem assist data submission? • Digital Lab Books (“MyEarthChem”) • Lab database • Automatic error checking • How do we ensure that data go to the appropriate data systems if they exist?

  22. Related (broader) Topics • How to include unpublished data? • How to ensure proper credit to data contributors • Assign unique identifiers to datasets (STD-DOI)? • Build “Data Citation Index”? • Access restrictions

  23. Outreach & Education • Outreach • Content & services of the EarthChem web site • Science applications • How to engage the community? • Newsletter, blog, twiki? • Town hall meetings • Workshop themes • Education • Short course GSA 2006 in Philadelphia • Posting of course projects on EC web site?

  24. EarthChem A community resource that facilitates the compilation, communication, serving, and visualization of geochemical & geochronological data www.earthchem.org

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