Linked Earth Wiki - User contributions [en]

Category:Lake Sediments Working Group

2017-06-24T16:20:00Z

Pfrancus: /* Sample Depth */

[[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 '''lake sediments''' (see [[:Category:LakeSediment | this page]] for a definition of the lake sediment archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].

__MEMBERS__

== Specific tasks ==
Thinking about data standards for lakes is a challenging task because of the incredible diversity of observations made on this archive. To start this process, the working group will focus on developing standards for the one variable in lake sediments that all scientists rely on: depth.

After we've done this process for depth, I suggest we reach out and broaden this group to include broad expertise of different sensor and observations types. A preliminary list is presented below.

== Task 1: Depth ==
How should we report depth?

[[File:MetadataDefinitions.png | thumb | right | 400px | Definition of essential, recommended, and desired in regards to paleoclimate data standards]]

For this discussion we recommend:
* structuring discussions around what scientific questions one would want to ask of the data
* listing essential, recommended, and desired 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''' 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

=== Sample Depth ===

'''Note''': Do not edit the polls (even for typos) once voting has started as it will reset the vote counts to zero. If a change needs to be made, make an annotation above the old poll (i.e., above the poll tags) and place the new poll below the first one.

In all cases, most simply, we want to report the geometry of a sample from a core. This requires two pieces of information, typically this is either the mid-point depth and thickness, or top and bottom depth. Each has its advantages:

*Top and bottom depth is more explicit and self explanatory, but typically requires an additional step to use for analysis
*Mid-point depth is more typically reported, and is what is needed for most age models, but can be ambiguous<br />

In the case of tilted or deformed sedimentary units (for instance due to coring operations), core depths should be read at the center of the core, and information regarding the width of the subsample should be reported.

[[File:LakeSediment Depth TwitterPoll.png|thumb|right|Results from Twitter Poll (3/14/17 to 3/21/17)]]

<poll>
What should be the primary way of reporting depth of samples taken from lake sediments:
Mid-point depth and thickness
Top and bottom depth
Something else
</poll>

'''The wiki and twitter polls indicate a slight preference for mid-point and thickness'''

=== Dealing with multiple cores ===
Commonly, multiple cores are used in a study that each have their own depth scale ("Core Depth") and using various methods, those depths are converted to "Composite Depth", which is used for most of the scientific inference. This is important additional information. We want:

#Mid-point depth (Core Depth)
#Mid-point depth (Composite Depth)
#thickness

and ideally, we want to store the necessary information that describes the relationship between core depth and composite depth.

LacCore (and others) use splice and affine tables to accomplish that.

Add a description and discussion of splice and affine tables for discussion here.

===Depth Datum===
For both core depth and composite depth, we need a datum for depth. Most typically, this is the top of the sediment in each core, for core depth (where depth=0), and is the sediment surface for composite depths. Sometimes, depth from the lake (water) surface is used.

We need to either

*Describe what datum is being used for each depth measurement
OR
*choose a universal datum and force datasets to adhere

Or we could do both.

== Sensors ==

Sensors in lakes fall into several different categories

=== Sediment ===
Several observations can be made on sedimentary sensors including:
*grain size
*mineralogy
*geochemistry
**bulk organic carbon concentrations
**bulk inorganic carbon concentrations
**bulk nitrogen concentrations
**C:N
*isotope geochemistry
**bulk organic carbon isotopic composition
**bulk inorganic carbon isotopic composition
**bulk nitrogen isotopic composition
**Compound Specific Isotopic Analysis (CSIA)
{| class="wikitable"
|-
|+Table 4: Essential/Recommended/Desired Metadata for Compound Specific Isotopes
|-
! Metadata || Essential (E)/ Recommended (R) / Desired (D) || Reason || Added by (optional)
|-
| [[:Category: Location_(L)]] (Lat, Lon) || E || Location is a must || [[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| | [[:Property:Wgs84:Alt (L)]] (Depth) || E || Water depth can be useful to get an idea of diagenesis in the core. Especially for deep-sea drilling sediments, water depths can be important to assess various biogeochemical properties || [[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| Sample Depth || E || Positional information needed to relate the samples back to the archive || [[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| ChonDataTable || E for new datasets/ R for legacy datasets || The raw radiocarbon, tie points, 210Pb measurements should be made available so that age models can be updated in light of new calibration curves or new age modeling techniques ||[[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| Compound(s) analyzed || E || e.g., n-alkanes, FAMEs, alkenones, dinosterol || [[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| Source of compound in sediments || R || Is this compound marine/aquatic or terrestrial in origin? || [[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| Isotope measured || E || e.g., ∂2H, ∂13C, ∂15N ||[[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
| Environmental Parameter CSIA is sensitive to || R|| Is the CSIA sensitive to salinity, precipitation, E-P, productivity, temperature? ||[[User:Jrichey|Jrichey]] ([[User talk:Jrichey|talk]]) 07:40, 24 April 2017 (PDT)
|-
|}

'''Note''': Do not edit the polls (even for typos) once voting has started as it will reset the vote counts to zero. If a change needs to be made, make an annotation above the old poll (i.e., above the poll tags) and place the new poll below the first one.

<poll>
For compound specific isotopes in lake sediments, should the compound analyzed be:
Essential Metadata
Recommended Metadata
Desired Metadata
</poll>

[[File:TwitterPoll LakeSediments CompoundIsotope Source.png | thumb | right | 400px | Results of the poll placed on Twitter from May 12th to 19th 2017]]

<poll>
For compound specific isotopes in lake sediments, should the source of the compound (terrestrial vs aquatic) be:
Essential Metadata
Recommended Metadata
Desired Metadata
</poll>

[[File:TwitterPoll LakeSediments CompoundIsotope Interpretation.png | thumb | right | 400px | Results of the poll placed on Twitter from May 12th to 19th 2017]]

<poll>
For compound specific isotopes in lake sediments, should the interpretation (e.g., temperature, salinity, precipitation) be:
Essential Metadata
Recommended Metadata
Desired Metadata
</poll>

=== Aquatic organisms ===
Several sensors may be found in lakes including
*Diatoms
**may contribute silicic microfossils and biomarkers
*Ostracods
**may contribute carbonate microfossils
*Algae
**may contribute biomarkers, including alkenones
*Archaea
**may contribute biomarkers, including GDGTs
*Bacteria
**may contribute biomarkers, including GDGTs
*Fish
**may contribute macrofossils, including otoliths

=== Terrestrial plants ===
Plants growing around the lake and in the catchment of the lake may contribute macro and microfossils as well as biomarkers to the sediments. Plants are the sensors of the environment and the observations include:
*Organic geochemical biomarkers:
**plant wax n-alkanes
**plant wax n-alkanoic acids
**plant wax n-alkanols acids
**plant wax terpenoids
**lignin
*Macro/microfossils
**pollen
**leaf
**wood
**charcoal

=== Insects ===
Several sensors in the air above and around lakes may leave microfossils in lake sediments, these include
* chironimid tests, these are organic microfossils

== Polls ==

Here are polls that the group might want to consider:

==References==
<references \>

Category talk:Lake Sediments Working Group

2017-06-24T16:16:05Z

Pfrancus: /* How should we report depth -- SimonGoring (talk) 11:33, 29 September 2016 (PDT) */

== How should we report depth -- [[User:SimonGoring|SimonGoring]] ([[User talk:SimonGoring|talk]]) 11:33, 29 September 2016 (PDT) ==

I think this isn't necessarily the right framing. The question should start with "how is depth reported".

There is legacy data in Neotoma (for example) that uses top or midpoint, but the depth basis isn't always clear. My preference would be to see both a depth field and a second "depthSectionBasis" field that would indicate "top" or "midpoint", followed with "thickness". From this you would then be able to obtain either top/bottom or midpoint, depending on your preference.

It would also allow you to manage legacy data, since these would not have the assigned "depthSectionBasis" terms. People could either revisit the primary literature and add the field, or you could treat "blank" fields in some special way.

The second element here seems to be that you haven't discussed depthBasis (I'm sure you've got a term somewhere). What is the depth baseline? Some of the cores in Neotoma use a depthBasis from the Lake Surface. This means they start at 2+m in some cases. This would also need to be defined in this schema.

In Goring et al., 2012 we specifically used only depth (and then the related geochronological data), from records that used pollen as a sensor.

We needed:

* sediment surface depth
* sample depth
* sample thickness

In a second proposal we suggested also knowing the basis of the depth measurement - is this from a single drive, or a composite record. Then you'd need to know the method for record alignment, the identity of the "upper" core section (possibly the identity of the next core section, but you could get that with a reverse lookup), the depth of alignment with the upper core section, & the depth of alignment within the target core section.

I'm worried by some of the conversation that says "we need to establish a standard", the standard should be full reporting, not stating that something is measured from lake floor. If we apply a standard then we fail with legacy data where reporting may not be fully describing the record.

Maybe it's the "standards" term, maybe it's better to describe "best practices"?

===Re: How should we report depth - Standard vs best practices -- [[User:Jeg|JEG]] ([[User talk:Jeg|talk]]) 20:49, 29 September 2016 (PDT)===

Thank you for initiating this. As someone who helps build ontologies, I'd be the first to agree that names matter. At the workshop we floated the idea of separate standards for legacy and new data. In my view, the standard for new data should be there to stimulate best practices. My $0.02.

===Re: How should we report depth -- [[User:Pfrancus|Pfrancus]] ([[User talk:Pfrancus|talk]]) 09:16, 24 June 2017 (PDT)===

I'm against reporting depth of samples taken with the mid-point and thickness, and this for 3 reasons.<br />

1. When establishing a composite depth, only two tie points in two different cores sections are reported as unique depths. If a sample is taken close to a tie point and reported using its mid-point and thickness, it is difficult to quickly assess if the sample is taken within or outside the composite section.<br />

2. Cores are drying and shrinking with time. If mid-point and thickness are reported, it is almost impossible to assess the exact sedimentary unit where the sample has been taken from, because shrinkage is seldom homogenous over a core section. That is not an issue for homogenous sediments, but it is critical for laminated sediments. Depth expressed as mid-point and thicknesses are way to ambiguous to me.<br />

3. I do not see the advantage of reporting the mid-point and thickness of a sample: there are still 2 numbers to enter in the database.

Category:Lake Sediments Working Group

2017-02-03T13:19:38Z

Pfrancus:

Category:Lake Sediments Working Group

2017-02-03T13:18:44Z

Pfrancus:

Category:Lake Sediments Working Group

2017-02-03T13:17:57Z

Pfrancus:

Category:Lake Sediments Working Group

2017-02-03T13:17:43Z

Pfrancus:

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2017-01-23T16:39:19Z

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2017-01-23T16:38:19Z

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2017-01-23T15:27:22Z

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