Prof Brent McInnes - Curtin university. IGSN in the Analytical Environment: Progress, issues and prospects, John de Laeter Centre, Curtin University.
2 Nov 2016, Canberra. International Geo-sample Number Symposium
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Brent McInnes, Warick Brown, Adam Brown, Matthias Liffers, Kelly Merigot, Cristina Talavera
IGSN in the Analytical Environment: Progress, Issues and Prospects
JdLC Digital Mineral Library Project
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Geochemical Data: Trends and Issues
Analytical innovation is producing multi-dimensional data sets at higher velocities and in
greater volumes (high-value spatial data)
Institutions are taking a greater interest in centralised custodianship of research data.
Data management via flash drive is not best practice (Research Office, ICT, Libraries)
Australian Research Council grant applications require data management, storage,
access and re-use plans (descriptive now, prescriptive later)
Structural transition from scholarly metrics based on citing of publications to citing of
publications and/or data (DataCite.org)
Publish or Perish in academia, but publications do not guarantee data discoverability
(estimated that only 15-30% of data gets published)
Social-cultural and operational issues around data sharing.
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A Vision of the Future
A digital information network for publicly funded institutions linking researchers,
physical samples, sample metadata, laboratory metadata, analytical data and
consumers.
15.12.2015Digital Mineral Library Project
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Researcher
A researcher may store their analytical
data on portable storage device or PC.
No machine metadata recorded.
Laboratory
A research lab may store data from
many users on lab or institutional
fileserver. No sample metadata
recorded.
Research Laboratory Practices - Status Quo
?
But what about the consumer?
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John de Laeter Centre
IGSN in the analytical laboratory - Issues?
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Progress in using IGSN in the laboratory:
Linking physical samples to analytical data
TIMA mineral analyser
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Research Data Australia metadata repository
IGSN
URI with IGSN
URI with IGSN
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200 mineral data sets publicly available,
plan to double in size by end of 2017
Digital Mineral Library Project
• New datasets available and
accessible for free:
• AuScope
• Research Data Australia
• Curtin Data Store
• Already being utilised by
GSWA, industry and
academia for MRIWA-
sponsored projects
• New research infrastructure
capable of being deployed
and utilised by any research
institution
AuScope Discovery Portal
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15.12.2015The Digital Mineral Library at Curtin University
AuScope Discovery Portal
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John de Laeter Centre
IGSN in the analytical laboratory - Issues?
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CRICOS Provider Code 00301J
Difference between mineral and rock mounts
require a change in labelling method
10 mm
TIMA mineral analyser
mount
(mineral grains)
SHRIMP mass
spectrometer mount
(zircon grains)
SHRIMP mount
(multiple samples)
SHRIMP mount
(multiple samples)
SHRIMP mount
(multiple plug samples)
SHRIMP mount
(multiple plug samples)
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RF-ID Tags in SHRIMP mounts
25 mm
Oxygen ion beam
focussed on top surface
SHRIMP operator needs
to see through mount to
Navigate around the grains
• Zircon grains extracted from rock
• U-Pb isotope concentrations
measured with SHRIMP
mass spectrometer
zircon grains
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RF-ID tags for a SHRIMP mount should be small
25 August 2015: CSIRO calls on researchers worldwide to join forces to save honey bees
Impinj Monza® 5 UHF RFID tag
Dimensions: 2.5 x 2.5 mm, weight 5.4 mg
EPC memory: Up to 128 bits, User memory: 32 bits TID memory: 48 bits
EPCglobal and ISO 18000-63 compliant, Gen2V2 compliant.
128 bits sufficient
to store ISGN
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Prospects
A digital information network for publicly funded institutions linking researchers,
physical samples, sample metadata, laboratory metadata, analytical data and
consumers.
IGSN, like ORC ID, is an important component of a digital information network
for Earth Sciences. Labs can readily incorporate both into analytical work flow
and data management systems.
Not the remit of analytical laboratories to be IGSN or ORC ID registry portals.
We need to make obtaining IGSNs easy, perhaps via a web services portal?
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Thanks to:
ANDS and AuScope, which are supported by the Australian
Government through the National Collaborative Research
Infrastructure Strategy Program.
Editor's Notes
JdLC has a large number of analytical instruments – third of them are shown here
These generate data in the areas of materials, surface physics, geochemistry and geochronology data for a range of research groups within the Curtin University, data to academic institutions, geological surveys and industry
I’m going to talk about samples and metadata related to U-Pb SHRIMP geochronology.
Besides the underpinning our understanding of earth history, geochronology is important for mineral exploration
This is because mineral deposit form in response to transient anomalous events that have quite a limited time span – like the change in lithospheric plate motion or a transition from compression to extension where 2 plates are colliding.
So to discover new ore deposits, it’s important to ensure that the rocks in the area being explored have an age that corresponds to the timing of those events
2 of the instrument used to determine the age of rocks are shown here at the right – one is called a TIMA – a mineral analyser and the other is type of mass spectrometer called a SHRIMP
In order to determine the age of rocks, we first need to located uranium bearing minerals in a rock sample. The instrument identifies the mineral species in the rock powder and colours an image of the sample according to a colde. This is done with the TIMA instrument pictured here. An example of the output is also shown
Sample and data management for this machine was the subject of a recently completed project.
Previously researchers might have scratched a number on the back of the epoxy mount and stored the data on a USB stick or C-drive of their computer
LIMS system designed to improve the situation was developed by Adam Brown based on Open data standards, software and development tools.
Rock powder is embedded on to the top of an epoxy block 25mm in diameter
International GeoSample Numbers (IGSN) allocated via SESAR are used to identify the samples.
These numbers together with the resolving service and IGSN prefix are contained QR-codes attached to the sample
Researchers to access the metsadata shown using a mobile phone QR-code reader app.
An example
<resolver>/<prefix>/<igsn>
The sample metadata is transferred from the LIMS or Laboratory Management System to ReDBox using csv files
A manual step involves Curtin Librarian minting a DOI for the analysis data set
Uploaded to RDA via Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) interface
You can see the metadata record here,
The URI based on the IGSN is shown lower down on the RDA webpage – here on the right
And the DOI is shown at the bottom.
The metadata is also displayed in spatial format on the AuScope Discovery Portal
The points show the locations where the original rock samples were collected in the field
Shown here by clicking on the TIMA data layer.
The user can click on any of the points to reveal the metadata for a particular sample
From here its also possible to download the data or individual samples or the entire sample collection.
JdLC has a large number of analytical instruments – third of them are shown here
These generate data in the areas of materials, surface physics, geochemistry and geochronology data for a range of research groups within the Curtin University, data to academic institutions, geological surveys and industry
I’m going to talk about samples and metadata related to U-Pb SHRIMP geochronology.
Besides the underpinning our understanding of earth history, geochronology is important for mineral exploration
This is because mineral deposit form in response to transient anomalous events that have quite a limited time span – like the change in lithospheric plate motion or a transition from compression to extension where 2 plates are colliding.
So to discover new ore deposits, it’s important to ensure that the rocks in the area being explored have an age that corresponds to the timing of those events
2 of the instrument used to determine the age of rocks are shown here at the right – one is called a TIMA – a mineral analyser and the other is type of mass spectrometer called a SHRIMP
Our current project involves extending the LIMS system to cover a new instrument
This is the SHRIMP instrument that I referred to earlier – once it’s established that uranium-bearing minerals are located in a sample –
The SHRIMP sample mount on the right has a much lower profile. We’ve experimented with smaller QR-codes to fit on this type of mount but they are too small to be read with a standard mobile phone app.
This led our current tests with Radio Frequency ID tags to store the IGSN numbers.
These tags are 5 to 10 mm long and about 3 -5 mm in height and width.
The tag is activated by proximity to an active reader – best if the tag is sitting directly in contact with the reader.
When the tag enters a reader’s RF field, the chip converts the induced electromagnetic field to the DC voltage that powers the chip.
We are testing these mounts in the SHRIMP.
The SHRIMP is a type of mass spectrometer that focusses a beam of oxygen ions on the upper surface of the samples (red arrow) using 20 kV in a vacuum.
So we’re testing to make sure that the RF-ID tag doesn’t cause any deflection of the ion beam (25 um) or interferes with the measurement of U/Pb isotopes
The ion beam doesn’t interfere with the RF-ID tag memory
You might have wondered why we can’t locate the QR-code labels on the back of the SHRIMP samples?
The reason is that in the analyst needs to look through the SHRIMP mount to see where the ion beam is located so we’d like to use RF-ID that are as small as possible –
This is an image of one of the smallest RF-ID chips available that is being used in a project at CSIRO. There are about 15,000 bees flying around with one of these.