Linked Earth Wiki - User contributions [en]

Category talk:Speleothem Working Group

2017-04-25T16:02:02Z

NickScroxton: answer to query

== Structure of Database and compatibility with SISAL, NOAA etc -- [[User:NickScroxton|NickScroxton]] ([[User talk:NickScroxton|talk]]) 09:25, 13 April 2017 (PDT) ==

In order to not reinvent the wheel its first good to understand the basics. Namely, the LiPD structure under which we will work

'''LiPD Format:'''
* Root Metadata: Dataset Name, Investigators, Link to online dataset, LiPD version
* Geographic Metadata: Coordinates, Sitename, Descriptive location (e.g. Country, State, Province, Ocean)
* Publication Metadata: Authors, Title, Journal, DOI, Year, URL
* Funding Metadata: Funding agency, Funding grant
* PaleoData Table: Measurement Tables (Column names, units and descriptions), Interpretation metadata, Calibration metadata, Models (Methodology used to produce the model results, Summary table of model output, Ensemble tables of data produced by the model, Distribution tables of data produced by the model)
* ChronData Table: Measurement Tables (Column names, units and descriptions), Models (Methodology used to produce the model results, Summary table of model output, Ensemble tables of data produced by the model, Distribution tables of data produced by the model)

As a speleothem working group, the largest difference between us and other groups will be Cave Metadata and Speleothem Metadata. Most of the rest will probably be fine with the LiPD standard (though this is a discussion so happy to hear thoughts).

The relevant metadata for the other major data depositories are:

'''NOAA Format:'''
* Publication Metadata: Authors, Title, Journal, Year, Volume, Edition, Issue, Pages, Report Number, DOI, Online Resource, Abstract, Alternative citations (for books, theses etc that don't fit above)
* Geographic Metadata: Site name, Location, Country, Northernmost latitude, Southernmost latitude, Easternmost longitude, Westernmost longitude, Elevation
* Data Collection Metadata: Name, Oldest Year, Youngest Year, Time Unit (yr BP etc), Core-length
* Species Metadata: (not relevant here)
* Funding Metadata: Funding Agency, Grant #
* Paleodata Table: relatively freeform with the following metadata: name, what, material (speleothem d18O, speleothem d13C etc), error, units, seasonality, data_type (speleothem), detail (raw, corrected), method, data format (numeric or type), Additional info
* ChronData Table: relatively freeform no additional metadata

'''SISAL Format:'''
* Publication Metadata: Citation, DOI
* Geographic Metadata: Cave Name, Latitude, Longitude, Elevation, Geology, Rock Age, Monitoring
* Stalagmite Metadata: Name, Overburden Thickness, Distance from Entrance, Speleothem Type, Drip Type, series of Yes/No for common proxies, Data DOI
* Paleodata Table: Stal Name, Distance from Top, Mineralogy, Composite (Yes/No), Equilibrium, Aragonite Correction, Age, Age Error, Age Model Type, Time Unit (yr BP etc), Annual Laminae Check, 14C deposition check, Sample Thickness, d13C measurement, d18O measurement, d13C precision, d18) precision, Isotope Standards (PDB, VPDB)
* DatingTable: Stal Name, Method, Depth, Thickness, Lab ID, Minimum Sample Weight, Maximum Sample Weight, UnCorr Age, UnCorr Age Error +, UnCorr Age Error -, Date used in age model, 238U, 238UErr, 232Th, 232Therr, 230Th, 230Therr, 230/232, 230/232err, 230/238act, 230/238acterr, Decay constants used, CorrAge, CorrAgeErr, Time Unit (yr BP etc), Year of Chemistry

The SISAL format is understandably a lot more prescriptive than the others as it is focused on speleothems.

My 2c: The LiPD format requires the LiPD Root Metadata. I also like the more detailed, Publication Metadata and Funding Data from LiPD. I would include the SISAL geographic metadata as our starting point, as a "Cave metadata" section. I think the biggest need in our field is for a "stalagmite metadata" section using SISAL as a start. I'd like to hear opinions as to whether we want freeform or prescriptive in the tables. My metadata opinion:
* Root Metadata: Dataset Name, Investigators, Link to online dataset, LiPD version
* Publication Metadata: Authors, Title, Journal, DOI, Year, URL
* Funding Metadata: Funding agency, Funding grant
* Cave Metadata: Cave Name, Latitude, Longitude, Elevation, Geology, Rock Age, Monitoring (Y/N)
* Stalagmite Metadata: Name, Overburden Thickness, Distance from Entrance, Speleothem Type, Drip Type, Data DOI

===Re: Structure of Database and compatibility with SISAL, NOAA etc -- [[User:Khider|Deborah Khider]] ([[User talk:Khider|talk]]) 13:38, 20 April 2017 (PDT)===

Thanks for starting the discussion, I added a few polls for community input in one of the sections.

We also updated the [[LinkedEarth Ontology]] and by extension LiPD to add information about the [[:Category:PhysicalSample (L) | Physical Sample]]. Perhaps some of the proposed properties specific to speleothems could be moved under this new category? I was thinking specifically about entity name, distance from cave entrance (in m), thickness of overlying bedrock above the speleothem (in m), speleothem type (candlestick stalagmite, stalagmite boss, flowstone), and drip type (seepage, seasonal, mixture, unknown).

== Reference (for each speleothem) [[User:Khider|Deborah Khider]] ([[User talk:Khider|talk]]) 14:46, 24 April 2017 (PDT) ==

Is this section supposed to contain the [[:Category:Publication_(L) | publication]] information of the study in which the speleothem record(s) appear(s) or is supposed to reference the [[:Category:PhysicalSample (L) | physical sample]] itself, for instance through a property like [[:Property:hasIGSN (L) | hasIGSN]].

===Re: Reference (for each speleothem) [[User:Khider|Deborah Khider]] ([[User talk:Khider|talk]]) 14:46, 24 April 2017 (PDT) -- [[User:NickScroxton|NickScroxton]] ([[User talk:NickScroxton|talk]]) 09:02, 25 April 2017 (PDT)===

I believe this would be the reference for the publication in which the speleothem record appears. The property for referencing the physical sample itself would be "entity name".

Category talk:Speleothem Working Group

2017-04-13T16:26:12Z

NickScroxton: /* Structure of Database and compatibility with SISAL, NOAA etc -- NickScroxton (talk) 09:25, 13 April 2017 (PDT) */

Category talk:Speleothem Working Group

2017-04-13T16:25:47Z

NickScroxton: /* Structure of Database and compatibility with SISAL, NOAA etc -- ~~~~ */ new section

== Structure of Database and compatibility with SISAL, NOAA etc -- [[User:NickScroxton|NickScroxton]] ([[User talk:NickScroxton|talk]]) 09:25, 13 April 2017 (PDT) ==

In order to not reinvent the wheel its first good to understand the basics. Namely, the LiPD structure under which we will work

'''LiPD Format:'''
* Root Metadata: Dataset Name, Investigators, Link to online dataset, LiPD version
* Geographic Metadata: Coordinates, Sitename, Descriptive location (e.g. Country, State, Province, Ocean)
* Publication Metadata: Authors, Title, Journal, DOI, Year, URL
* Funding Metadata: Funding agency, Funding grant
* PaleoData Table: Measurement Tables (Column names, units and descriptions), Interpretation metadata, Calibration metadata, Models (Methodology used to produce the model results, Summary table of model output, Ensemble tables of data produced by the model, Distribution tables of data produced by the model)
* ChronData Table: Measurement Tables (Column names, units and descriptions), Models (Methodology used to produce the model results, Summary table of model output, Ensemble tables of data produced by the model, Distribution tables of data produced by the model)

As a speleothem working group, the largest difference between us and other groups will be Cave Metadata and Speleothem Metadata. Most of the rest will probably be fine with the LiPD standard (though this is a discussion so happy to hear thoughts).

The relevant metadata for the other major data depositories are:
'''NOAA Format:'''
* Publication Metadata: Authors, Title, Journal, Year, Volume, Edition, Issue, Pages, Report Number, DOI, Online Resource, Abstract, Alternative citations (for books, theses etc that don't fit above)
* Geographic Metadata: Site name, Location, Country, Northernmost latitude, Southernmost latitude, Easternmost longitude, Westernmost longitude, Elevation
* Data Collection Metadata: Name, Oldest Year, Youngest Year, Time Unit (yr BP etc), Core-length
* Species Metadata: (not relevant here)
* Funding Metadata: Funding Agency, Grant #
* Paleodata Table: relatively freeform with the following metadata: name, what, material (speleothem d18O, speleothem d13C etc), error, units, seasonality, data_type (speleothem), detail (raw, corrected), method, data format (numeric or type), Additional info
* ChronData Table: relatively freeform no additional metadata

'''SISAL Format:'''
* Publication Metadata: Citation, DOI
* Geographic Metadata: Cave Name, Latitude, Longitude, Elevation, Geology, Rock Age, Monitoring
* Stalagmite Metadata: Name, Overburden Thickness, Distance from Entrance, Speleothem Type, Drip Type, series of Yes/No for common proxies, Data DOI
* Paleodata Table: Stal Name, Distance from Top, Mineralogy, Composite (Yes/No), Equilibrium, Aragonite Correction, Age, Age Error, Age Model Type, Time Unit (yr BP etc), Annual Laminae Check, 14C deposition check, Sample Thickness, d13C measurement, d18O measurement, d13C precision, d18) precision, Isotope Standards (PDB, VPDB)
* DatingTable: Stal Name, Method, Depth, Thickness, Lab ID, Minimum Sample Weight, Maximum Sample Weight, UnCorr Age, UnCorr Age Error +, UnCorr Age Error -, Date used in age model, 238U, 238UErr, 232Th, 232Therr, 230Th, 230Therr, 230/232, 230/232err, 230/238act, 230/238acterr, Decay constants used, CorrAge, CorrAgeErr, Time Unit (yr BP etc), Year of Chemistry

The SISAL format is understandably a lot more prescriptive than the others as it is focused on speleothems.

My 2c: The LiPD format requires the LiPD Root Metadata. I also like the more detailed, Publication Metadata and Funding Data from LiPD. I would include the SISAL geographic metadata as our starting point, as a "Cave metadata" section. I think the biggest need in our field is for a "stalagmite metadata" section using SISAL as a start. I'd like to hear opinions as to whether we want freeform or prescriptive in the tables. My metadata opinion:
* Root Metadata: Dataset Name, Investigators, Link to online dataset, LiPD version
* Publication Metadata: Authors, Title, Journal, DOI, Year, URL
* Funding Metadata: Funding agency, Funding grant
* Cave Metadata: Cave Name, Latitude, Longitude, Elevation, Geology, Rock Age, Monitoring (Y/N)
* Stalagmite Metadata: Name, Overburden Thickness, Distance from Entrance, Speleothem Type, Drip Type, Data DOI

Category:Speleothem Working Group

2017-04-11T20:26:37Z

NickScroxton: minor edit

[[Category:Working Group]]

== Overview ==
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for [[:Category:Speleothem | speleothems]], and aims to formulate a set of recommendations for such a standard.

== Membership ==
__MEMBERS__

== Specific tasks ==

We recommend that discussions focus on the following techniques, and explore potential commonalities.

For each observation type, we recommend:
* structuring discussions around what scientific questions one would want to ask of the data
* listing essential, recommended, and optional information for:
** the measurements themselves
** any inference made from the measurements (e.g. calibration to temperature)
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)
* provide an '''ideal data table''' (or [[Cyrstal2013.paleo1measurement1 | link to one]]) for each type of observation, so the community knows what to report and how to report it.
* provide separate recommendations for new and legacy datasets

== Things to describe ==
=== Observations ===

* stable isotopes
* trace metals
* organics
* fluid inclusions
* mineralogy
* clumped isotopes
* noble gas temperatures
* C14
* Optical Density of luminosity (ODL)
* Mg/Ca

=== Modern Cave Conditions ===
The interpretation of geochemical or lithological signals embedded in speleothem archives relies sometimes heavily on implicit assumptions about cave hydrology.
What parameters need to be archived to enable long-term re-use and better information extraction from speleothem datasets?

Above-Cave
* soil thickness
* vegetation type

In-Karst Hydrology
* karst residence time
* transit time distributions
* porosity
* rock overburden thickness
* flow route type

In-Cave
* Temperature
* Humidity
* pCO2
* drip-rate
* drip chemistry

=== Chronology ===
Please see the [[:CategoryChronologies_Working_Group| chronologies WG]] for generalities about U/Th dating or layer-counting.
If challenges specific to dating speleothems exist, please list relevant metadata properties below.

* For age models based in lamina counting, evidence that laminae are annual
* For age models using C14 for deposition rate, evidence on robustness of assumed linearity

=== Sample data ===

* Distance from top of speleothem
* Thickness of analysed sample
* Evidence of equilibrium (Hendy tests)
* Year (with uncertainty)

==References==
<references \>

Category:Speleothem Working Group

2017-04-11T20:25:01Z

NickScroxton: Expanded hydrology section to include all modern observations

[[Category:Working Group]]

== Overview ==
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for [[:Category:Speleothem | speleothems]], and aims to formulate a set of recommendations for such a standard.

== Membership ==
__MEMBERS__

== Specific tasks ==

We recommend that discussions focus on the following techniques, and explore potential commonalities.

For each observation type, we recommend:
* structuring discussions around what scientific questions one would want to ask of the data
* listing essential, recommended, and optional information for:
** the measurements themselves
** any inference made from the measurements (e.g. calibration to temperature)
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)
* provide an '''ideal data table''' (or [[Cyrstal2013.paleo1measurement1 | link to one]]) for each type of observation, so the community knows what to report and how to report it.
* provide separate recommendations for new and legacy datasets

== Things to describe ==
=== Observations ===

* stable isotopes
* trace metals
* organics
* fluid inclusions
* mineralogy
* clumped isotopes
* noble gas temperatures
* C14
* Optical Density of luminosity (ODL)
* Mg/Ca

=== Modern Cave Conditions ===
The interpretation of geochemical or lithological signals embedded in speleothem archives relies sometimes heavily on implicit assumptions about cave hydrology.
What parameters need to be archived to enable long-term re-use and better information extraction from speleothem datasets?
A few come to mind:

Above-Cave
* soil thickness
* vegetation type

In-Karst Hydrology
* karst residence time
* transit time distributions
* porosity
* rock overburden thickness
* flow route type

In-Cave
* Temperature
* Humidity
* pCO2
* drip-rate
* drip chemistry

=== Chronology ===
Please see the [[:CategoryChronologies_Working_Group| chronologies WG]] for generalities about U/Th dating or layer-counting.
If challenges specific to dating speleothems exist, please list relevant metadata properties below.

* For age models based in lamina counting, evidence that laminae are annual
* For age models using C14 for deposition rate, evidence on robustness of assumed linearity

=== Sample data ===

* Distance from top of speleothem
* Thickness of analysed sample
* Evidence of equilibrium (Hendy tests)
* Year (with uncertainty)

==References==
<references \>

Nick Scroxton

2016-11-08T19:11:42Z

NickScroxton: Added PropertyValue: Expertise = Speleothem paleoclimatology

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Current Affiliation=University of Massachusetts Amherst|
Current Position=Postdoctoral Research Scholar|
Expertise=Speleothem_paleoclimatology|
Has User ID=NickScroxton|
Subscribes To=Category:Speleothem_Working_Group|
Twitter ID=@StalagNick}}

Nick Scroxton

2016-11-08T19:11:25Z

NickScroxton: Added PropertyValue: Current Position = Postdoctoral Research Scholar

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Current Affiliation=University of Massachusetts Amherst|
Current Position=Postdoctoral Research Scholar|
Has User ID=NickScroxton|
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Nick Scroxton

2016-11-08T19:11:17Z

NickScroxton: Added PropertyValue: Current Affiliation = University of Massachusetts Amherst

[[Category:Person_©]]{{#set:
Current Affiliation=University of Massachusetts Amherst|
Has User ID=NickScroxton|
Subscribes To=Category:Speleothem_Working_Group|
Twitter ID=@StalagNick}}

Nick Scroxton

2016-11-08T19:11:05Z

NickScroxton: Added PropertyValue: Twitter ID = @StalagNick

[[Category:Person_©]]{{#set:
Has User ID=NickScroxton|
Subscribes To=Category:Speleothem_Working_Group|
Twitter ID=@StalagNick}}

Nick Scroxton

2016-11-08T19:09:52Z

NickScroxton: Added PropertyValue: Subscribes To = Category:Speleothem_Working_Group

Nick Scroxton

2016-11-08T19:09:44Z

Nick Scroxton

2016-11-08T19:09:44Z

NickScroxton: Added PropertyValue: Has_User_ID = NickScroxton