DATA SYSTEMS FOR SAMPLE- BASED OBSERVATIONS 1 Kerstin Lehnert
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- DATA SYSTEMS FOR SAMPLE- BASED OBSERVATIONS 1 Kerstin
Lehnert
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- Data from Samples Distributed data acquisition Different
labs/researchers analyze the same sample or subsamples of it.
Distributed data publication Different data for the same sample are
published in different papers. Distributed data archiving Data for
the same sample are kept in different data systems. Integrated data
access required to maximize utility. 3
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- Geochemical Data diverse hundreds of parameters thousands of
materials vary with space and time over a range of more than ten
orders of magnitude complex mostly sample-based with complex
relations among samples & subsamples distributed data
acquisition (one sample analyzed in different labs by different
researchers at different times) Idiosyncratic data acquisition
methods 4
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- Geoinformatics for Geochemistry DATABASES thematic geochemical
databases (PetDB, SedDB, VentDB) DATA REPOSITORY Geochemical
Resource Library REGISTRIES System for Earth Sample Registration
SESAR IEDA Data Publication Agent of the STD-DOI system (DataCite)
GeoPass: single sign-on authentication system DATA ACCESS &
ANALYSIS TOOLS GfG user interfaces EarthChem Data Engine (Portal)
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- EarthChem XML DB Metadata catalog datasets (original data &
derived products) GCDM DB GfG Architecture 6 USGS NAVDAT GEOROC
EarthChem Portal GfG Data Entry User Submission External Databases
Topical Data Collections Geochemical Resource Library
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- GeoChemical Data Model 7 observed value publicationdata source
method/DQ sample feature of interest collection, geospatial
analysis material preparation, obs. point
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- Metadata Geospatial Geographical coordinates Geographical names
Collection Sampling technique Field program Description & Age
Classification Texture Alteration Age Data Quality Technique
Instrument Laboratory Precision Reference material measurements
Correction procedures
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- Standards for Data Access & Integration WMS, WFS For
visualization tools OAI-PMH For joint data inventories EarthChemML
For integration across geochemical data systems For
interoperability with other systems 16
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- IEDA System-wide Inventory Inventory Expedition Metadata
Reference Metadata Dataset Metadata Geospatial Metadata RSS feed
MGDS SESAR EarthChem GRL Geochem DBs Object Registration Object
Metadata Object Registration Object Metadata Chemical Data Cruise
Info Chemical Data Cruise Info DOI Registration
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- EarthChem Portal 19 PetDB Others USGS GEORO C NAVDA T EarthChem
Data Engine Database XML EarthChem Data Engine Search &
Visualization Partner databases encode their data & metadata in
XML and send them to the EarthChem portal database in Kansas.
Queries submitted at the EarthChem portal search the contents of
the EarthChem Portal Database.
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- Access Levels
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- EarthChemML
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- EarthChem Repository: user submission need tools that are easy
to use and support the data flow from lab to publication ideally,
represent pipelines for data capture early in the data acquisition
process tools need to include data validation and DQC procedures
offer citable data publication need data policies 23
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- IEDA data publication service 24
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- STD-DOIs The STD-DOI metadata are mainly Dublin Core elements,
plus data specific elements. The metadata transmitted to the
National Library via web service (HTTP/SOAP) and incorporated into
the library catalogue. The metadata may contain references to other
objects (DOI, IGSN,...): Element isCited, isParent, isChild,
isDuplicate, 25
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- STD-DOIs The element can be used to point to other electronic
objects: Point to the literature where the data set is interpreted.
Point to samples, from which the data were derived. Point to other
datasets that belong to the same collection of datasets. These
links can be used by machines (e.g. data portals) to make search
suggestions and thus aid discovery of data, literature and samples,
or other added value services. 26
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- STD-DOI System Architecture
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- Data DOIs 28
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- Information Discovery Link to publication Citation of data IGSN
points to sample
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- The International GeoSample Number 30
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- Ambiguous Sample Naming Examples from the PetDB Database Sample
names are duplicated. Sample names are modified or changed. Sample
names are duplicated. Sample names are modified or changed.
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- Provides & manages unique identifiers for samples IGSN -
International Geo Sample Number Assigned upon registration of
sample metadata Catalogs & archives sample metadata Access to
sample metadata via web site & web services Long-term
preservation of metadata Link to sample archives Facilitates links
to data IGSN will be incorporated into persistent resolvable
GUIDs
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- IGSN:SIO8JH3M4 International GeoSample Number A Global Unique
Identifier for Earth Samples Strict syntax (9 digits, alphanumeric)
First three characters are unique user code (registered with SESAR)
Last 6 characters are random numbers + letters Allows 2,176,782,336
sample identifiers per registrant Does not replace personal or
institutional names. Applied to samples & sub-samples system
tracks relations 33 www.geosamples.org Name space
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- Geoinformatics for Geochemistry Core Core Section 1 Core
Section 3 Core Section 2 Sample 1 Sample 2 Sample 1 Sample 2 Sample
3 Sample 1 Sample 2 Sample 3 Rock powder Mineral conc. Leachate
Fossil separate Microprobe mount Parent Child Parent IGSN:XXX000120
IGSN:XXX0065B3 IGSN:XXX9K23G6 IGSN:XXX07ST4K IGSN:XYZ0G693M
IGSN:ABC0L98SW IGSN:ABC0L53NW IGSN:ABC0L653X IGSN:ABC078HGB
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- Sample Types Sampling events such as holes, cores, dredges,
stratigraphic sections Individual samples: specimens rocks,
minerals, fossils, fluid samples, precipitates, synthetic material,
etc. Sub-samples of any of above: processed samples such as mineral
or fossil separates, leachates, thin sections, etc.
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- Sample Registration Spreadsheet forms for batch loading
Interoperability (web services) Interoperability SESAR Web
Site
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- Implementation Challenges Diversity of users Large sampling
campaigns (IODP, ICDP, ECS) Repositories Data systems Individual
investigators Diversity of sample types Integration into existing
policies, procedures, data systems International scope Connectivity
in the field 37
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- Solutions Schema improvements Web-service based registration
from client data systems Distributed system of registration nodes
(Trusted Agents) Handle service for IGSNs (persistent, resolvable)
http://dx.doi.org/18.2539/IGSN.SIO001234
http://dx.doi.org/18.2539/IGSN.SIO001234 Tools to facilitate
registration iSESAR (registration via iPhone) eCollections
(personal sample management) webCollections (hosting services for
repositories) IGSN International Consortium 38