iscn / soc-drahr Goto Github PK

Visualization and Analysis of Microbial Population Structures (Open Source License)

avoorhis_VAMP

Todo;

• Review and Decide if Useful for the Main Project

Copied from NSCN-support message:

Hi,

I have just logged in to the ISCN database for the first time for a while.

I downloaded the data from Iceland, and realised the data is actually from Puerto Rico.

Also there is no data from the UK, which surprised me. Is there no data for the UK, or has the data been miss-labelled ?

Thanks,

Kevin.

========================================

Kevin Coleman
Sustainable Agriculture Sciences
Rothamsted Research
Harpenden, AL5 2JQ

Direct line: +44 (0)1582 938494
E-mail: [email protected]

Rothamsted Carbon Model: https://www.rothamsted.ac.uk/rothamsted-carbon-model-rothc

ResearcherID: D-5271-2011 http://www.researcherid.com/rid/D-5271-2011
ORCID ID: https://orcid.org/0000-0002-9640-1479

Ingest the ISCN 3 database from here: http://iscn.fluxdata.org/

• Read in Layer data

• Read in Profile data

• Read in Meta data

• Make template and vocabulary machine readable

• Map site locations (lat-lon, state (no lat-lon) totals, country (no lat-lon) totals)

• Histograms of all data by type

New data from Natural Resources Canada. Current version of db is personal communications with @ktoddbrown but an manuscript is in submission (Oct 2016).

• Key variables to ISCN
• Convert units
• Visualize variables

Hi,

Let me know if you would like to coordinate with the AQP project, we may have invented a couple of wheels that you are more than welcome to use.

Specifically:

• SoilProfileCollection S4 classes / methods
• interfaces to NCSS soil databases
• re-sampling methods via aqp::slice() and aqp::slab()
• soil profile vizualization

Details at the AQP website

Cheers,
Dylan

The SOC [g cm-2] calculations for US O-horizon layer data may be very off by orders of magnitude. Go back, recalculate form bulk density and organic carbon, and possible flag buggy variables.

Investigate possible hook with the Teabag index folks:
https://www.mail-archive.com/[email protected]/msg55503.html

Layer_name is not a unique identifier in ISCN3. For example, site_name: NE260-1-NH layer_name:68001.1 Looks like a .10 got truncated to .1 by Excel.

Need to go back to the processing script and add lat-lon-layer_top-layer_bottom-observation_date to the identifiers to prevent this from happening again.

Data from: Changes in plant, soil and microbes in a typical steppe from simulated grazing: explaining potential change in soil carbon

Liu N, Kan H, Yang G, Zhang Y

Date Published: January 20, 2015

DOI: https://doi.org/10.5061/dryad.q428q

The data were collected in the field. Excel was used to create the data. SE-standard error, MBC-soil microbial biomass carbon, MBN- soil microbial biomass nitrogen. Treatment: C- control,DU-dung and urine return; M-mowing; T-trampling; DU+M-mowing combined with the addition of dung and urine; M+T-mowing combined with trampling; DU+T-trampling combined with the addition of dung and urine; DU+M+T-mowing combined with trampling and the addition of dung and urine

http://datadryad.org/resource/doi:10.5061/dryad.q428q

Script out 'timestamp header' as a variable to read in so we can go back and change at latter dates as needed.

Bulletin series 1590

soil chronosequence data - Data is in PDF format but there is recognized text. Consider stripping tables using R's package pdftools::pdf_text or something similar.

Lange, Markus; Steinbeiss, Sibylle; Habekost, Maike; Gleixner, Gerd; Luo, Guangjuan; Guderle, Marcus; Meyer, Sebastian Tobias (2015): Collection of data on soil carbon (particulate and dissolved) in the Jena Experiment (Main Experiment, time series since 2002). PANGAEA, link

This should include a walk through on

• key development
• the different sections of soilDataR::processData_Templet.R

Data set being pushed as SI in https://www.elsevier.com/books/advances-in-agronomy/sparks/978-0-12-812415-4 by Geoffery Davies and Elham Ghabbour. Check back after October 1 2017.

Berhe AA, Harden JW, Torn MS, Kleber M, Burton SD, Harte J (2012) Persistence of soil organic matter in eroding versus depositional landform positions. Journal of Geophysical Research: Biogeosciences, 117, n/a-n/a.

Dataset coded as an example in association with USGS Powell Center soil carbon working group

• translate variables to ISCN/PC
• convert units
• visualize

Want to minimize repeated information while maintaining flexibility to read in survey data, field manipulations, and lab treatments.

Key to keep attributes like data set DOI (DOI == set_id??) and ORCID for data providers, include manuscripts (optional).

http://datadryad.org/resource/doi:10.5061/dryad.p83h7

Title Plant and soil data from the last year of the biodiversity experiment
Data from: Wen-feng Cong, Jasper van Ruijven, Liesje Mommer, Gerlinde De Deyn, Frank Berendse and Ellis Hoffland. (2014) Plant species richness promotes soil carbon and nitrogen stocks in grasslands without legumes. Data were collected in the 11-year grassland biodiversity experiment in Wageningen, the Netherlands, in 2010 and 2011. Abbreviated headlines are as follows: “”BLK”= block; “PT”= plot; "SR" = plant species richness; “MI” = monoculture identity (Ac = Agrostis capillaris; Ao = Anthoxanthum odoratum; Cj = Centaurea jacea; Fr = Festuca rubra; Hl = Holcus lanatus; Lv = Leucanthemum vulgare; Pl = Plantago lanceolata; Ra = Rumex acetosa); "AAB" = average aboveground biomass from 2000 to 2010 (g m-2); "RB" = standing root biomass (g fresh weight m-2) up to 50 cm depth in June 2010; "CS" = soil carbon stocks (g C m-2) in April 2011; "NS" = soil nitrogen stocks (g N m-2) in April 2011. "CD" = soil organic carbon decomposition (mg CO2-C kg-1 soil) measured in soil collected in April 2011; "NM" = potential net N mineralization rate (µg N kg-1 soil day-1) measured in soil collected in April 2011.

Dataset to add:

Tibetan plateau C stocks study
https://doi.pangaea.de/10.1594/PANGAEA.833208

WHRC-TNC project modeling spatial extent of soil carbon loss due to agriculture

Check that this is the original data provider. Regardless be sure to cite as ingested data in some fashion.

Measures of microbial, soil and plant variables of three grass-based agro-ecosystems in Austria, the UK and France (underrepresented regions)

https://doi.pangaea.de/10.1594/PANGAEA.879537

This is a soil map of microorganisms using taxonomy and traits, from Lennon JT, Aanderud ZA, Lehmkuhl BK, and Schoolmaster DR (2012) in Ecology 93.

LennonLab Soil Mapping

Current Need;

• Search and Decide on Use of Repository
• Pull Dataset

Port over each ISCN 4 data contributor from here.

Main manuscript
Data + code

field fertilization, crops, SOC w/ depth

http://datadryad.org/resource/doi:10.5061/dryad.f4m6k

When using this data, please cite the original publication:

de Blécourt M, Corre MD, Paudel E, Harrison RD, Brumme R, Veldkamp E (2017) Spatial variability in soil organic carbon in a tropical montane landscape: associations between soil organic carbon and land use, soil properties, vegetation, and topography vary across plot to landscape scales. SOIL 3(3): 123-137. https://doi.org/10.5194/soil-3-123-2017
Additionally, please cite the Dryad data package:

de Blécourt M, Corre MD, Paudel E, Harrison RD, Brumme R, Veldkamp E (2017) Data from: Spatial variability in soil organic carbon in a tropical montane landscape: associations between soil organic carbon and land use, soil properties, vegetation, and topography vary across plot to landscape scales. Dryad Digital Repository. https://doi.org/10.5061/dryad.f4m6k

Worth checking to see how many studies from the Gracenet/REAP database have been ingested into ISCN.

GraceNet - Greenhouse gas Reduction through Agricultural Carbon Enhancement network, Agriculture Research Service project data http://usdaars.maps.arcgis.com/apps/MapSeries/index.html?appid=9415d09247f64ae5bde462a3a9292e6c

Del Grosso, S. J., J. W. White, G. Wilson, B. Vandenberg, D. L. Karlen, R. F. Follett, J. M. F. Johnson et al. "Introducing the GRACEnet/REAP data contribution, discovery, and retrieval system." Journal of environmental quality 42, no. 4 (2013): 1274-1280.

I'll look at the key between the current data structures. This is an aggregation of other studies with their own doi's - will need to check for duplication.

Data from: Intensive forest harvesting increases susceptibility of northern forest soils to carbon, nitrogen and phosphorus loss

Hume AM, Chen HYH, Taylor AR (2017) Intensive forest harvesting increases susceptibility of northern forest soils to carbon, nitrogen and phosphorus loss. Journal of Applied Ecology, online in advance of print. https://doi.org/10.1111/1365-2664.12942

http://datadryad.org/resource/doi:10.5061/dryad.dd602

Link: http://harvardforest.fas.harvard.edu:8080/exist/apps/datasets/showData.html?id=hf005
doi:10.6073/pasta/429cdb44b6932caf2c30071957a75a2a

Forest Inventory and Analysis National Program
Is this already in ISCN3?

Make it all into an R package that can install from git

One-meter soil cores were taken to evaluate soil texture, bulk density, carbon and nitrogen pools, microbial biomass carbon and nitrogen content, microbial respiration, potential net nitrogen mineralization, potential net nitrification and inorganic nitrogen pools in 32 residential home lawns that differed by previous land use and age, but had similar soil types. These were compared to soils from 8 forested reference sites.

link to metadata
link to data

Data are published in:
Raciti, S. R., P. M. Groffman, J. C. Jenkins, R. V. Pouyat, and T. J. Fahey. 2011a. Controls on nitrate production and availability in residential soils. Ecological Applications:In press.

Raciti, S. R., P. M. Groffman, J. C. Jenkins, R. V. Pouyat, T. J. Fahey, M. L. Cadenasso, and S. T. A. Pickett. 2011b. Accumulation of carbon and nitrogen in residential soils with different land use histories. Ecosystems 14:287-297.

This is a soil organic carbon analysis on the carbon levels in soil within fermented forests.

pskoulgi/SOCanalysis

Todo;

• Review and Decide if the Data will be Useful to the Master Project

Bader 2017 6 month peat incubation at 10C and 20C 560 samples 21 sites (crop, grass, forest) Switzerland. CO2 measurements and basic SOM characterization

• Submit data request to authors (with request for data doi)

Should we start some webscraping activity to pull files directly from the web rather than download them manually? I know the idea is to have all of this data integrated into ISCN, but if we're going to be data hacking as an ongoing process, it might be easier to check each other's scripts more easily without having to go download the data ourselves.

This is a soil radiocarbon meta analysis with 150+ data points from several different studies.

He et al Science 2016

Current need:

• Contact study author to confirm which data to include in study (assigned KTB)
• Copy over SI Table 2
• Write data ingest

From the data submitted for ISCN vs4:
data

Peat properties synthesis dataset (2MB, XLSX format, download only; ISCNtemplate_Treat_peatProps_v2): This dataset is a synthesis of literature and site-level data on peat properties, C, N, 14C, and vegetation from 366 sites worldwide. Data are available for nearly 16,000 layers from 659 profiles. Data contributed by Claire Treat.

• Data ingestion
• write test script
• visualization report

Do we want to insist on a certain units? Should ingestion scripts do any unit conversion? What about flux/concentration normalization in ingestion scripts?

Flux by volume, mass, or total incubation measure?
SOC vs OC vs BD?

This is a micro and macro analysis on the affect of soil fungal communities by nitrogen fertilization and grassland plant communities.

Note; this paper is still in submission.

ITS_soil_landuse_aggregate

Todo;

• Review and Decide if Data is Useful for the Master Project

Soil dataset for eastern China (underrepresented region) study in rice paddies

Here's the dataset on dryad http://datadryad.org/resource/doi:10.5061/dryad.6m11c

Here's the paper
http://onlinelibrary.wiley.com.stanford.idm.oclc.org/doi/10.1890/14-0189.1/full

Data from: Interactions among roots, mycorrhizae and free-living microbial communities differentially impact soil carbon processes

Moore JAM, Jiang J, Patterson CM, Wang G, Mayes MA, Classen AT

Date Published: October 21, 2015

DOI: https://doi.org/10.5061/dryad.pb271

Soil respiration, soil carbon pools, and enzyme activities. The first row is a header and units of measurement are included in this row. In "exclusion group", R=roots and M= mycorrhizae. In "carbon label", C=control (water-only) and L=labeled starch addition.

FYI This repo is going to archived and relevant parts merged with soilDataR which is now https://github.com/ISCN/SOCDRaH_soilDataR Hopefully this will reduce redundancies and smooth out the development pipeline.