petdb seddb earthchem sesar - marine geo...petdb data collection for geochemistry & petrology of...

PetDB SedDB

EarthChem SESAR

GfG Digital Data Collections

Objective: develop, maintain, & operate community-driven, sustainable information systems that

support the long-term preservation of dataenable data discovery and use for the broad communityadvance a culture of “open access” to data (& samples) and the creation of a global data networksupport data analysis to empower sciencefacilitate data integration via interoperability & open access interfaces

GfG Projects

PetDBData Collection for Geochemistry & Petrology of Ocean Floor Igneous & Metamorphic Rocks

SedDBData Collection for Geochemistry of Marine Sediments

EarthChemGeochemistry Information Network

SESARRegistry for Earth Samples

Administration of global unique identifiers for samplesGlobal Sample Catalog

Grants

PetDB SedDB EarthChem SESAR GfG/MGDS Management

K. LehnertK. Block

K. LehnertS. L. Goldstein

Subcontracts:R. Murray (BU)N. Pisias (OSU)W. Snyder (Boise State)

K. Lehnert

Collaborative withD. Walker (U Kansas)

K. LehnertS. L. GoldsteinS. VinayC. Lenhardt

K. LehnertS. Carbotte

Sept 2007ToAug 2010

Jul 2005ToJun 2008

Sept 2005ToAug 2010

Apr 2006ToMar 2009

Apr 2007ToMar 2010

Budgets

SedDB23%

GfG Mgmt16%

SESAR21%

PetDB

EarthChem17%

Salaries76%

Subcontracts13%

Participant support4%

Travel5%

Other1%

Hardware&Software1%

FY2008: $983,669

GfG Components

1. Information Technology Services2. Data Management3. Community Building4. Education

PetDBSedDB

EarthChemSESAR

EarthChem

1. IT Services

Database Development & AdministrationModeling & metadata standards for geochemical and sample dataData submission tools & proceduresQC & data ingestion tools & proceduresMaintenance of databases

Access InterfacesWeb application development & maintenanceInteroperability (web services, xml development)Visualization & data analysis tools

Systems Operation & Maintenance

LDEO/CIESIN: Sri Vinay (Ass. Director), Robert Arko, Branko Djapic, Brian Falk, Annie Gerard, Yuanliang Liu, Frank Pascuzzi, David Strom U Kansas/KGS: Jason Ash, Eileen Jones

Built architecture that is used across all GfG projects.Will make operation and enhancement of existing systems and development of potential future systems more efficient, cost effective, and sustainable.

Toward an Integrated GfG System

GenericModularFlexibleScalableSecure

Geochemical Data ModelImplementation completed for SedDB 1.0Will be implemented for EarthChem in Fall 2007Will be implemented for PetDB in Winter 2007/8

Analytical metadata at the level of individual measurements Description of spatial and temporal components of samples and measurementsAbility to integrate data at any level of sample granularityTracking of relationships between samples and sub-samplesCapability to store ‘derived’ (model) types of observed valuesGeoSciML compliant

Geochemical Data Framework

Framework for executing complex queries against a geochemical relational databaseConsists of database query models and data cache that supports the web interfaces and web servicesDeveloped using Object Oriented Design (OOD) methodologies on a Java/J2EE platform supported by WebLogic application server

Implementation for SedDB 1.0 (alpha)Implementation for PetDB in Summer 2008

Web Services

Analytical Data ServingEarthChem XML (ECML) and GeoSciML

Geospatial Data ServingWMS/WFS implemented for PetDB dataWMS/WFS for SedDB by AGU Fall 2007SESAR Samples

Data Loading ServicesGeochemical Data validation and loading

Implemented for PetDB, SedDB, EarthChemSESAR Sample registration via external systems (e.g. IODP)

IT Services: 2007 Highlights

New hires: Frank Pascuzzi, Yuanliang Liu, & Brian Falk

Redesign/restructuring of all GfG web sitesConsistent architecture/menu items across all projectsAddition of event list application

SedDB 1.0 alpha releaseSESAR Catalog Search alpha releaseImproved EarthChem XML schema & portal interfaceSESAR XML schema for IODP sample registrationWMS/WFS for PetDB in GeoMapAppMap interfaces for PetDB, SedDB, SESAR

Redesign of GfG web sites

SedDB 1.0 (alpha)

SESAR Catalog Search (alpha)

IT Services: Foci for the Next Year

PetDB: Migration to the new GfG architectureSESAR

SESAR Catalog Search: move to productionWeb application for MyGeosamplesWeb application for online sample registration

SedDBSedDB 1.0: move to productionWMS/WFS for cores and specific datasets (MARGINS focus sites)Implementation of tools developed at Boise State

Geochemistry Data Library

Geochemistry Data Library - WDC

Repository for datasets‘Raw’ datasets ingested into data collectionsElectronic supplements from journalsData compilations submitted by PIs

Request from journals to serve electronic supplements with geochemical data

GeologyGeological Magazine

Enhances long-term archiving of data collections

“iGeoCuration” SESAR Online Sample Curation System

Service to repositories/museums to manage their collections and provide public access

Modules to manage administrative metadata (e.g. storage, acquisition, loans, collections)Service to develop & operate public & administrative web interfaces to collections

Advantages for repositories:No IT infrastructure & IT personnel neededNo maintenance and risk & contingency management neededAccess from anywhere by authorized individualsPlatform independent

Contract with Harvard Geological Museum Interest by Marine Repositories

2. Data Management

Data solicitationData compilation & documentationData entry & ingestionQuality ControlUser support

LDEO/CIESIN: Karin Block, Annika Johansson, Rusty Lotti, Branko Djapic, Brian FalkInterns: Maxine Paul, Peregrine Gerard-Little

Integrating Data Ingestion

Redesigned data entry forms to accommodate requirements of Geochemical Data Model

Common for all data collectionsImplemented for SedDB 1.0Challenge: Data management needs vs. community acceptance

Adjusted DataEndorser to new data entry forms

Data Management: 2007 Highlights

Compiled & ingested ca. 150,000 chemical values to PetDB, SedDB, EarthChem datasets

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Deep Lithosphere DatasetCompiled & ingested complete Wilshire (1988) xenoliths dataReceived new voluntary data submissions (Ducea, Lee, Basu, Ionov, Klump)Developing chemistry-based classification for peridotite xenoliths based on the dataset

Collaboration with R. Stern, M. Ducea, E. AnthonyPhD student Urmidala Raye (UT Dallas) internship at GfGPresentation by K. Block at AGU 2007

Workshop at EarthScope National Meeting (Monterey, March 2007)

Convened by K. Lehnert, M. Ducea, R. Keller, K. BlockAttended by 20 peopleRecommendation for future developments/expansion of dataset


New EC Dataset: Central Atlantic Magmatic Province (CAMP)

Collaboration with Claude Herzberg (Rutgers University)Trained Rutgers undergraduate students in data management & compilation18 publications compiled and enteredData will be available from PetDB and EarthChem

New SedDB Dataset: Global Mn-nodule Chemistry

USGS Open File report by F. ManheimDefinitive dataset for Mn nodules (ca. 750 samples)Compiled by undergraduate Maxine Paul, research with dataset is planned QuickTime™ and a

TIFF (LZW) decompressorare needed to see this picture.

Data Management: Success & Challenges

Voluntary contributions increasing (PetDB, CAMP, Deep Lithosphere)Increased number of NSF requests to PIs to submit data

Need policy for unpublished data / moratorium periodsNeed data submission templates & proceduresIncreased user support

Data Management: Foci for 2008

Test & improve data submission templatesDefine policies & procedures for data submissionMigrate PetDB data to GCDMMigrate Deep Lithosphere Dataset to GCDMComplete SedDB compilation of test bedsGrow EarthChem datasetsEncourage voluntary contributions

3. Community BuildingGoals

Achieve broad use & involvementImprove integration of data across systems, disciplines, organizational, & political structuresCreate new organizational structures to support, manage, and operate a Geoinformatics infrastructure

Approaches & ActivitiesUnderstand the social & cultural challengesEducate & involve the user communityDevelop & promote technical solutions & policiesAugment partnerships & collaborationsEncourage & participate in community efforts

Understand the Social & Cultural Challenges

Collaboration with social & information scientists

Educate & Involve Community

Workshops, Courses, Exhibits, Presentations, AC

4 EarthChem Workshops1 SESAR workshop2 Short Courses4 Exhibits

AGU 2006Goldschmidt 2007

PublicationsNewsletters / list serversWeb sites

Educate & Involve Community

ESF Field Workshop Barberton Drilling Project, Sept 2007ESF Field Workshop Barberton Drilling Project, Sept 2007

Upcoming Presentations

GSA 2007 (Oct 28-31)Lehnert: "My Data. Your Data. Our Data! - Overcoming Cultural Barriers to Open Data Sharing”Lehnert: “The PetDB Data Collection: Impact on Science” (poster)Walker: "EarthChem: New Developments”

Joint MARGINS-IFREE Workshop IBM SubFac (Nov 9-11)

Block: “Online Geochemical Database Resources for Teaching: The Subduction Factory and Beyond”Johansson: “SedDB - A Global Geochemical Database of Marine Sediment Geochemistry”Lehnert: “Databases - US Perspective”

AGU 2007 (Dec 10-14)Lehnert: “Community-Based Development of Standards for Geochemical and Geochronological Data”Lehnert: “Building a Global Data Network for Studies of Earth Processes at the World's Plate Boundaries”Block: “A Chemistry-Based Classification for Peridotite Xenoliths”Block: “Fostering Education and Research Goals Through Partnerships Between

Upcoming Short Courses

GSA 2007, DenverTuesday, Oct 30, noon

AGU 2007, San FranciscoSunday, Dec 9, 2-5pm

Develop & Promote Technical Solutions & Policies

Data & Metadata Standards

EarthChem Working Groups & Workshops

Defined standards and templates for data reporting.“Reporting of Geochemical Data and Metadata” (Lamont, April 2007)“GeoEarthScope and EarthChem - EARTHTIME Effort” (Kansas, April 2007)“EarthChem: (U-Th)/He Geo/Thermochronology” (Kansas, May 2007)Metadata Type Relevance Example

Measured Parameter mandatory 87Sr/86Sr Technique mandatory TIMS Instrument optional VG Laboratory mandatory Washington State Univ Analyst optional J. Vervoort Analysis Date optional 03/17/2006 Sample Preparation optional Ground in agate mill Chemical Treatment optional Leached in 1N HCL Reference Sample Name mandatory NSB-987 Reference Value Measured mandatory 0.710246 Reference Uncertainty mandatory 0.000017 Reference Uncertainty Unit mandatory 2 sigma absolute Number of Measurements Averaged (N) mandatory 24

Primary Analytical Metadata


Interoperability Standards

Development & ImplementationGeoSciML -OGC (WMS, WFS) implemented for PetDB, SedDBXML (EarthChemXML, SESAR registration)Controlled vocabulariesIGSN implementation


IGSN ImplementationSESAR Workshop “Implementing the International Geo Sample Number in Geological Sample Curation”

Established procedures for sample registration.Trusted Agents (e.g. IODP)Pre-populated MGDS forms

IGSN implemented at NGDC Index of Marine & Lacustrine Samples.Collections registered

ScrippsWHOILamontODP/DSDPURIARFUSPRRHarvard


Policies

New Geochemical Society Data PolicyInitiated at Goldschmidt 2006, approved at Goldschmidt 2007

Editors Roundtable, Goldschmidt 2007Reached agreement among editors of major scientific journals on the principles of a joint policy for data publication.To be approved at Goldschmidt 2008.

GSA-GPPC Open Access Working Group


“Global Data Networks” workshop (Kiel, May 2007), covened by S. Carbotte, K. Lehnert, S. Tsuboi, W. Weinrebe

Agreed on statements of principle and recommendations to addresstechnical, procedural, and organizational issues of open global data sharing.

Partnerships & CollaborationsNational

LEPR: Integration with experimental dataInterop proposal with State Surveys & USGS (“Geosciences Information Network”)GEON: SedDB in Paleo Integration ProjectNGDC: IGSN implementation, marine repositories

InternationalGEOROC - Germany (Al Hofmann, Baerbel Sarbas)GFZ Potsdam - Germany/International (Jens Klump)Mexico: MexDB (Luca Ferrari)China: Eastern China Geochemical Database (Shan Gao)South Africa: Economic Geology Research Institute (Allan Wilson)Australia: Geoscience Australia (Lesley Wyborn), CSIRO (Simon Cox)

Community OrganizationPlanning a National Geoinformatics System

Organization of NSF workshop (Walker)Participation in NGS Task Force & WG (Walker, Lehnert, Vinay)NGS Planning proposal to EAR July 2007Co-convened AGU 2006 Town Hall meeting (Lehnert)Co-convened GSA 2007 Town Hall meeting (Walker, Lehnert)

Community Building: Tasks 2008

Short courses at regional universities & collegesEditors Roundtable Goldschmidt 2008Science session at Goldschmidt 2008

Conveners: Lehnert, Salters, KubickiEGU 2008 Workshop with ICDP/IODP: “Data Infrastructure for Scientific Drilling”International Working Groups

Follow-up of Kiel workshopAdvance EarthChem International Network (workshop?)

Involvement in NGS

Summer Interns 2007Maxine Paul (Columbia University): SedDBUrmidola Raye (UT Dallas): EarthChem (w/ R. Stern)Naya Sou (Rutgers University): EarthChem - CAMP dataset (w/ C. Herzberg)Stephanie Bloomer (Rutgers University): EarthChem - CAMP dataset (w/ C. Herzberg)Peregrine Little-Gerard (Columbia University): EarthChem, PetDB

4. Education

CoursesInternshipsEducational materials

Metrics of SuccessUser statistics

PetDB: 2000-2500 unique users per monthEarthChem: from a few hundred to ca. 1100 unique users/mths

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are needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

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Citations28 publications in 2007 citing PetDB, 168 publications since 20005 publications citing EarthChemToo early for SedDB, need complete dataset

EarthChem Statistics

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petdb seddb earthchem sesar - marine geo...petdb data collection for geochemistry & petrology of...

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