Determine if and how various soil type/classification/taxonomy terms will be used in the submission schema

[mslarae13]

soil_taxonomic/local classification method
soil_taxonomic/local classification
soil_type
soil type method
soil_taxonomic/FAO classification
link to classification information
-- Removed?

These slots are very similar. We should discuss these slots and provide clearer separation between the types and better guidance on how to use / identify

Resolution

• Provide Montana an export from NCBI of metadata records that included this field and how they wrote it (@turbomam )
• Evaluate usage of these slots across database and determine if all are being used / how (Montana)
• examples and guidance are added to slot usage (Montana)
• Implement these changes to NMDC submission portal (Mark & Kitware

[turbomam]

• fao_class
• local_class
• local_class_meth
• soil_type
• soil_type_meth
• see also
  • Determine if and how link_class_info will be used in the submission schema #678

[turbomam]

From GSC

https://github.com/GenomicsStandardsConsortium/mixs/blob/main/mixs/excel/mixs_v6.xlsx

Environmental package	agriculture	soil
Structured comment name	fao_class	fao_class
Package item	soil_taxonomic/FAO classification	soil_taxonomic/FAO classification
Definition	Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups	Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
Expected value	enumeration	enumeration
Value syntax	{term}	[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]
Example		Luvisols
Requirement	C	X
Preferred unit
Occurrence	1	1
MIXS ID	MIXS:0001083	MIXS:0001083

In production NMDC MongoDB

db.getCollection("biosample_set").find( { fao_class : { $exists : true } } );

0

In BBOP relational version of NCBI's biosample_set

select
	value,
	count(1)
from
	all_attribs aa
where
	aa.harmonized_name = 'fao_class'
group by
	value
having
	count(1) > 1
order by
	count(1) desc;

value	count
Cambisol	516
not applicable	444
not collected	431
rendzina	368
Oxisol	301
Typic Hapludalfs	270
Luvisols	264
Mollisol	232
Endostagnic Luvisol from glacial till	192
using EC meter (HORIBA) with a 2:5 soil/water suspension	192
Haplic Chernozem	170
Histic Andosol	160
Chernozem	143
Hoytville silty clay loam	133
Kokomo silty clay loam	132
calcaric leptic cambisols	131
Phaeozem	126
Fluvisol	120
sandy loam	104
cambisol	101
chernozem	100
Greyzemic Phaeozem Albic	97
"Fine-silty, mixed, thermic Oxyaquic Fragiudalfs"	96
"Fine, mixed, active, mesic Typic Paleudalfs"	90
mesic Lamellic Hapludalfs	90
Typic Argiudoll	88
loess	80
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 1:10 soil/water suspension (mS cm-1)	78
NA	72
Vitric eutric epiarenic	72
missing	67
Typic Argiudolls	66
podzol	64
Podzol	59
Luvisol	56
Andosol	56
Luvic Phaeozem	54
Nitisol	51
Typic Hapludalf	48
Arenosol	48
"Fine-loamy, mixed, subactive, thermic typic Hapludults"	47
Calcaric, Eutric Fluvisol	36
Umbric Epistagnic Albeluvisol	36
Leptosol	36
Gleysol	36
Histosol	34
Cryosol	31
3a	30
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 1:5 soil/water suspension	30
Haplic Phaeozem	27
Pellic Vertisol	27
Ferralsol	25
arenosols	24
Stagnosol	22
sod-podzolic	22
Earth-cumuli-Orthic Anthrosols	21
Chromic Luvisol	21
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 2:5 soil/water suspension (mS cm-1)	20
na	19
Calcisols	18
andosol	17
Mottled Fragic Pallic Soil (Ustochrept)	16
loess chernozem	16
Vertisol	14
Regosol	12
Planosol	12
Oxisols	12
Cambisols	10
Phaozem	9
0	6
Haplic Luvisol	6
Isbell 2002	6
Geric Ferralsol	5
Stagnic Cambisol	4
Cambisol (almost Ferralsol)	3
Umbrisol	3
loamy-skeletal, mixed, active, mesic Lithic Dystrudept	3
Kastanozem	3
histosol	3
fluvisol	3
Lithosol	3
phaeozem	2
gypsisol	2
vertisol	2
ferralsols	2

[turbomam]

Environmental package	agriculture	soil
Structured comment name	local_class	local_class
Package item	soil_taxonomic/local classification	soil_taxonomic/local classification
Definition	Soil classification based on local soil classification system	Soil classification based on local soil classification system
Expected value	local classification name	local classification name
Value syntax	{text}	{text}
Example
Requirement	C	X
Preferred unit
Occurrence	1	1
MIXS ID	MIXS:0000330	MIXS:0000330

value	count
not collected	432
not applicable	415
3% humus, 22 % clay, 38 % silt	324
clayish	293
Freeon silt loam	264
Wahiawa	253
Medial-skeletal, amorphic, mesic Humic Haploxerand	243
Waialua	232
sandy loam, 3.5 % humus	216
sandy loam	204
Coarse-loamy, mixed, superactive, mesic Humic Dystroxerept	200
Rego Black Chernozem	192
2% humus, 21 % clay, 32 % silt	180
Loamy-skeletal, mixed, superactive, mesic Typic Haploxerept	177
silty clay loam	166
dark brown forest soil	162
NA	137
KaC	135
OsD	135
Rendzina (RR)	120
histosol	105
Orthic Humo-Ferric Podzol	99
Flanagan silt loam	96
Bloomfield	90
Brown coniferous forest soil	67
missing	65
Typic Argiudoll	54
Typic Argiudoll, with a silty clay texture	47
Typic Dystrudepts	45
Fluvaquentic humaquept	36
Sandy loam	30
Entic Haplustoll	27
Argic Pelludert	27
Aquic Glossudalfs	23
Histic Pergelic Cryaquepts	23
Mesic Ultic Haploxeralfs	23
Brunisolic Gray Luvisol	21
Orthic Dystric Brunisol	21
Rudisol	20
na	18
candler fine sand	17
Sterling-Sheep Creek-Richmond-Foxol-Elzinga-Agassiz (s7785)	16
loess chernozem over limestone	16
Dermosol	15
Brown Andosol	14
Histic pergelic cryaquept	12
Nielsen-Dranyon-Dra (s2168)	12
Latossolo vermelho	12
Lithocalcic Calcarosol	12
Clay loam to silty clay loam over clay with flints	12
Gravelly Vitrisol	11
taylorsflat loam	8
Typic cryorthent	6
Rock outcrop-Henefer-Harkers-Gappmayer (s7849)	6
Rock outcrop-Mower-Lundy-Lizzant-Hamtah-Agassiz (s8168)	6
Travessilla-Rock outcrop-Midfork family (s7972)	6
Stafford loamy fine sand	6
Steed-Redola-Provo-Pleasant View-Pleasant Vale-Keigley (s7862)	6
Yeates Hollow-St marys-Moweba-Hoskin-Holmes (s7833)	6
Vertosol	5
aeolian sediment	5
Calcarosols	4
Calcarosol	4
Roundy-Fitzgerald-Daybell (s7884)	3
Yeates Hollow-Lucky Star-Hoskin-Horrocks-Gappmayer-Cloud Rim-Bradshaw-Ant Flat (s7886)	3
Lithic Udorthents	2
Vertosol (grey)	2
Tenosols	2
Paleudult	2
Paleudalf	2

db.getCollection("biosample_set").find( { local_class : { $exists : true } } );

0

[turbomam]

Environmental package	agriculture	soil
Structured comment name	local_class_meth	local_class_meth
Package item	soil_taxonomic/local classification method	soil_taxonomic/local classification method
Definition	Reference or method used in determining the local soil classification	Reference or method used in determining the local soil classification
Expected value	PMID,DOI or url	PMID,DOI or url
Value syntax	{PMID|DOI|URL}	{PMID}|{DOI}|{URL}
Example
Requirement	C	X
Preferred unit
Occurrence	1	1
MIXS ID	MIXS:0000331	MIXS:0000331

value	count
USDA Soil Survey Taxonomy (2003)	620
Swiss Federal Research Stations FAL RAC FAW, 1996. Swiss Reference Methods of the Federal Agricultural Research Stations. Soil and Substrate Research for the Fertilizer Advisory Service (Arable, Fodder, Fruit Farming, Viniculture and Horticulture), vol. 1. Swiss Federal Research Stations.	504
not collected	432
not applicable	415
SoilWeb	270
USDA soil classification	264
VDLUFA Methodenbuch, D 2.1, ISO 10694:1995	216
http://soils.usda.gov/technical/classification/taxonomy	214
NA	137
Bodenkundliche Kartieranleitung (Ad-hoc-Arbeitsgruppe Boden der Staatlichen Geologischen Dienste und der Bundesanstalt für Geowissenschaften und Rohstoffe)	120
INTA soil map (http://geointa.inta.gov.ar/visor/?p=model_suelos)	108
NRCS	96
missing	65
Australian Soil Classification	30
na	19
World Reference Base for Soil Resources (WRB)	16
Isbell, 2002, The Australian Soil Classification, revised edn (CSIRO Publishing: Melbourne)	15
EMBRAPA	12
Isbell, R.F. 2002 The Australian Soil Classification. Melbourne, CSIRO Publishing.	12
websoilsurvey.sc.egov.usda.gov/App/WebSoilSurvey.aspx	6
Santos, H.G., Jacomine, P.K.T., Anjos, L.H.C. dos, Oliveira, V. ., Lumbreras, J.F., Coelho, M.R., Almeida, J.A., Cunha, T.J.F., Oliveira, J.B., 2014. Sistema brasileiro de classifica o de solos, 4th ed. Embrapa, Bras lia, DF.	6
Argiudol typic/USDA Soil Taxonomy	5
Argiudol vertic/USDA Soil Taxonomy	4
Haplustol entic/USDA Soil Taxonomy	4

db.getCollection("biosample_set").find( { local_class_meth : { $exists : true } } );

0

[turbomam]

Environmental package	agriculture	food-farm environment	soil
Structured comment name	soil_type	soil_type	soil_type
Package item	soil type	soil type	soil type
Definition	Soil series name or other lower-level classification	Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.	Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.
Expected value	soil type name	ENVO_00001998	ENVO_00001998
Value syntax	{text}	{termLabel} {[termID]}	{termLabel} {[termID]}
Example		plinthosol [ENVO:00002250]	plinthosol [ENVO:00002250]
Requirement	M	X	X
Preferred unit
Occurrence	1	m	1
MIXS ID	MIXS:0000332	MIXS:0000332	MIXS:0000332

value	count
Cambisol	1815
pine_forest	1632
Luvisol	1281
M21	1266
fine sandy loam	733
silt loam (2-4% slopes; fine-silty, mixed, superactive, mesic mollic oxyaquic hapludalf)	708
Inceptisol	636
not applicable	609
Pond Creek fine sandy loam (Pachic Argiustoll)	530
loam	466
not collected	437
Crop	390
NA	385
Rozetta silt loam	336
forest	319
50:50 mixture of steam-sterilized native soil and Metro-Mix 200 growing media	314
Agricultural Mollisol from a Fallow Casssava Field	312
Rhizosphere	309
Thrice Heat Steriled River Sand	306
Bulk	296
sandy loam	291
bulk	282
desert	270
grassland	266
Freeon silt loam	264
Rendzic Leptosol and Chromic Cambisol	256
arable sandy soil	254
SoilB	248
SoilA	245
Andesite	243
Strip	240
away	234
alfisol	227
Luvisol WRB	222
Orthic Black Chernozem	222
Pecatonica silt loam	216
Udalfs	214
alluvial sandy soil	213
Coarse-loamy.mixed.active.mesic_Typic_Dystrudepts	211
Eluviated dystric brunisol	210
Granite	200
Missing: Not provided	190
rhizosphere	189
Sandy	185
Haplic Phaeozem	184
Basalt	177
fine mixed thermic Cumulic Haplustoll	176
Xerolls	175
American ginseng continuous cropping obstacle soil	174
control	172
Arensols and Luvisols	170
canna coco	170
SoilC	168
-	168
SoilD	168
Albi-Boric Argosols	162
Coarse-loamy_over_sandy_or_sandy-skeletal.mixed.active.mesic_Typic_Dystrudepts	161
sandy soil	160
Eutric Fluvisol	159
Chernozem	156
promix	150
home	139
Not applicable	136
Hoytville silty clay loam	133
bulk soil	132
Kokomo silty clay loam	132
unfamiliar	131
10% field soil inoculum	124
Rendzina (RR)	120
sandy clay loam	120
Sand	119
Alluvial	110
Haplic Kastanozem	108
water	108
missing	101
familiar	97
Greyzemic Phaeozem Albic	97
Cultivated soil	96
Fallow soil	96
loam Acrisol	96
Loring B2 series	96
clay Acrisols	95
Lush serpentine	94
rhizosphere soil	92
Maury silt loam	90
Harsh serpentine	86
Non-serpentine	84
Ultisol	81
Mollisol	81
Orthic Humic Gleysol	80
phaeozems	80
histosol	78
sandy silty clay	78
clay	74
Rich Lake	73
loam Acrisol with long periods of stagnating water	72
Silty Clay Loam	72
Typic Ustivitrands	72
Ultic Hapludalf/Typic Fragiudult	72
saline-alkali soil	70
loamy sand	69
Brown Forest soil	68
Bori-Udic Cambosols	67
Typic Mesisol	65
loess chernozem over limestone	64
Regosol	63
Fort Collins loam	61
Mollisols	60
O	60
Hyposodic Vertisol	60
Chromic Luvisol	60
Interface	60
Luvic-Phaeozem	60
Loamy Sand	60
Residual	57
Gleyic-Fluvisol	56
SG	56
Typic Argiudoll	54
saneli silty clay loam	54
cambisol	53
FF	52
Soddy podzolic	52
black earth	52
Arenic-Luvisol	52
Mor	51
Bulk_soil	49
Leptosol	49
Submerged_zone	48
cultivated soil	48
agricultural	48
corn	48
RV	48
nitisol	48
Top_sediment	48
clay acrisol	48
coarse loamy inceptisol	48
switchgrass	48
Shady	47
loam acrisol	47
luvisol	46
Dystric cambisol	45
Clay	44
D	40
L	40
red_soil (south of China)	40
soil_type not involve	40
black_soil (north of China)	40
Nonserp	40
Silty_Clay_Loam	39
S+NSmic	39
Sandy_Loam	38
Brownzems raw-humic illuvial-humic	38
calcareous ?uvo-aquic soil	37
Sodosol	37
1	37
Mountain-meadow soddy	36
Rice Soil	36
Serp	36
Manure	36
Loamy	36
Forest Soil	36
NS+Smic	36
Rich	35
Poor	35
silty clay	35
Silt	35
Stagnosol	34
Xeralfs	34
Gray Brown Luvisol	33
Eutric Fluvisols	33
Cancienne silt loam	32
Leaf litter residuum	32
mycobiome	32
Canton	30
Mesic Typic Argiudoll	30
Sandy loam	29
Calcisol	28
stony silty clay loam	28
Loessal Soil	28
silty clay loam	28
Eum-Orthic Anthrosols	28
Albic Luvisol	28
calcareous fluvo-aquic soil	27
Mor-moder	27
cambsiol	27
Captured Dust	27
Argic Pelludert	27
Gypsum	27
Sandy_loam	27
Bulk Soil	27
Elstow orthic dark brown loam	27
Silty Loam	27
sand	27
Entic Haplustoll	27
Vertisol	24
Limnic Humisol	24
Silt loam	24
Acrisol	24
Mollic Psammaquent	24
continuous cropping soil	24
Haplic Planosol	24
rotational cropping soil	24
Cast	24
Rhizo	24
Orthents	23
pristine peat soil	23
clayey	23
soil sample	23
Silty	23
Medium Soil	21
silt	21
Andosol	21
Alluvials saturated	21
"CA"	21
N/A	20
black soil	20
Cutanic Luvisol developed from glacial till	20
Gray lowland soil	20
"CL"	19
Loam	19
3	19
mollisol	19
sandy clay	19
Mountain-meadow sod-peaty	19
na	18
Black soil	18
Podzol soil	18
Rich Soil	18
A	18
clayey sand	18
G	18
S	18
Sediment	18
Orthic Gray Luvisol	17
mineral soil	17
inceptisol	17
Groundwater sediment	17
Soil fertilised with sludge	17
Soil fertilised with slurry	16
Macdonald	16
monomicrobial soil	16
Soil fertilised with mineral	16
Stages of soiling	16
mixed microbial soil	16
Organic	16
control (sterilized) soil	16
Leptosol /Sand	16
Soil fertilised with usw	16
oxisol	16
BNC	15
BRR	15
CAG	15
Poor Soil	15
BPP	15
Gloucester	15
Loess	15
BB	15
CCS	15
6	14
Chernozems leached mycelial-calcareou	14
Broun Forest soil	14
Xerepts	14
podzol	13
aridisol	13
Leptosol Umbric Petrocalcic Gleyic/Sand	12
unplanted soil	12
drained peat soil	12
typical Clay loamy Fe-leachic-gleyic-stagnic anthrosol	12
Rhizosphere soil of watermelon planted in forest soil	12
Rhizosphere soil of watermelon planted in rice soil	12
Leptosol Umbric Calcaric /Sand	12
Karshner	12
acid red	12
Without pathogens	12
Standard soil Lufa 2.3	12
Rhizosphere soil of cucumber planted in forest soil	12
Soil of apple orchard	12
basalt of volcanic origin	12
sandy-loam from silicate substrate	12
stony clay loam	12
stony silty clay	12
Rhinebeck silt loam	12
Leptosol Umbric Calcaric Nudilithic/Sand	12
Rhizosphere soil of cucumber planted in rice soil	12
Leptosol Umbric Calcaric Gleyic/Sand	12
4	11
Alluvials compact	11
2	11
Orthic Gleysol	11
Fill	10
5	10
Root soil interface	10
Bastsil	10
Upper Scarp Complex	9
NS+Smic+Ni	9
Marine	9
Fernwood (Arenosol)	9
Ferric-Udic Cambisols	9
Griffin (Gleyic Acrisol)	9
Typic Hapludands	9
"ST"	9
Bekenu	9
Merit	9
NS+Smic+Drought	9
Histic Epiaquands	9
Leptosol/Sand	8
Pinedene (Helvic Acrisol)	8
silt loam	8
Clay loam	8
Clay loamy endogleyic-Fe-leachic-stagnic anthrosol	8
Nyalau	8
potting soil	8
moraine	8
Humults	8
Phaeozem Luvic/Loam	8
Organic Soil	8
Peat	7
Rendzina	6
Aquepts	6
Rhizosphere soil of celery planted in rice soil	6
Rhizosphere soil of celery planted in forest soil	6
Poor Lake	6
not collection	6
with F.oxysporum	6
sod podzol	6
Original rice soil	6
Saprists	6
Argids	6
red earth	6
PLcomparison	6
Bath	6
Original forest soil	6
Hudson silt loam	6
Ferric-Ustic Luvisols	6
Podzol	6
Stafford loamy fine sand	6
Houston	6
Olnes	6
sandy	5
furrow soil of potato plant with low common scab severity level	5
silty loam	5
geocaulosphere soil of potato plant with high common scab severity level	5
rhizosphere soil of potato plant with low common scab severity level	5
Anthroposol	5
ultisol	5
andisol	5
Nixon Sandy Loam	5
Aquents	5
rhizosphere soil of potato plant with high common scab severity level	5
root-zone soil of potato plant with high common scab severity level	5
root-zone soil of potato plant with low common scab severity level	5
geocaulosphere soil of potato plant with low common scab severity level	5
Williamson	5
Water	4
Mesic Organic Cryosol	4
eutric endostagnic cambisol	4
n/a	4
gelisol	4
furrow soil of potato plant with high common scab severity level	4
Portneuf silt loam	4
Sandy Loam	4
entisol	4
Albeluvisol	4
gleyed slightly humic	4
Leptosol/ Sand	4
Lordstown	4
Langford	4
deep sandy loam (top soil) 30cm, med-heavy clay (80-100cm)	3
Typic Torriorthent	3
granite	3
Pe+LTNDT N1K1 Field	3
Clay Loam- Clacium Carbonate	3
Typic Vitrandept	3
Pe+LTNDT M1P1 Field	3
LTNDT M1P1 Field	3
Pe+LTNDT N1P2K2 Field	3
Loam over clay over limestone	3
High sand sandy loam over yellow/red clay	3
Loam over clay	3
Loam over red clay	3
Deep Friable Gradational clay loam	3
M	3
Hapludox	3
Entic Cryandept	3
Pe+LTNDT N2P2K2 Lab	3
Bubbly loam	3
Thick sand over clay	3
LTNDT M1P1 Lab	3
Dystric Xerocrept	3
Initial soil, with no fertilization nor chemical nor organic	3
Sandy loam over yellow Pudsolic clay	3
Clay Loam over red clay	3
None	3
Red/brown earth - stone fragments -strong clay over shift	3
Typic Haplohumult	3
alluvium	3
LTNDT N1K1 Field	3
healthy soil	3
LTNDT N1P2K2 Field	3
Meadow dirt- high organic carbon content	3
Red brown earth over red clay	3
Sand over red clay	3
Erie	3
Pe+LTNDT M1P1 Lab	3
Dry soil	3
LTNDT N2P2K2 Lab	3
water control	3
Shallow top soil- red clay/Limestone	3
clay loam over red clay with various calcium carbonate layers	3
Sandy loam over blocky clay	3
Red/Brown earth	3
Sand over yellow/orange clay	3
Sandy alluvial	3
agricultural soil	2
tar sand	2
desert gypsum	2
Mixed Waste Organic Output	2
pine forest	2
Lts	2
Volusia	2
blank	2
spodosol	2
Harper series, thermic Lithic Haplustolls, Mollisol	2
Ornithic Leptosol	2
Kendaia	2
Eckert series, thermic Lithic Haplustolls, Mollisol	2
tundra soil	2
Gray Solodized Solonetz	2
Biochar	2
Real series, thermic Typic Calciustolls, Mollisol	2

db.getCollection("biosample_set").find( { soil_type : { $exists : true } } );

0

[turbomam]

Environmental package	agriculture	food-farm environment	soil
Structured comment name	soil_type_meth	soil_type_meth	soil_type_meth
Package item	soil type method	soil type method	soil type method
Definition	Reference or method used in determining soil series name or other lower-level classification	Reference or method used in determining soil series name or other lower-level classification.	Reference or method used in determining soil series name or other lower-level classification
Expected value	PMID,DOI or url	PMID,DOI or url	PMID,DOI or url
Value syntax	{PMID|DOI|URL}	{PMID}|{DOI}|{URL}	{PMID}|{DOI}|{URL}
Example		Frederick series; Weikert series
Requirement	M	X	X
Preferred unit
Occurrence	1	1	1
MIXS ID	MIXS:0000334	MIXS:0000334	MIXS:0000334

value	count
Gray	708
parent material	620
USDA taxonomy	555
not applicable	536
not collected	438
NA	373
WRB	353
Canadian System of Soil Classification	290
USDA soil classification	264
USDA Soil Taxonomy system	254
According to soil characteristics	174
FAO 1998	170
-	168
Bodenkundliche Kartieranleitung (Ad-hoc-Arbeitsgruppe Boden der Staatlichen Geologischen Dienste und der Bundesanstalt für Geowissenschaften und Rohstoffe)	120
Webster_silty_clay_loam	120
INTA soil map (http://geointa.inta.gov.ar/visor/?p=model_suelos)	108
missing	101
USDA soil taxonomy	73
World Reference Base system	72
IUSS	72
Web Soil Survey, USDA	61
World Reference Base System	61
USDA	49
soil_type_meth not involve	40
US Taxonomy	33
The Canadian System of Soil Classification, 3rd edition	33
Web of soil survey	32
FAO-WRB	28
more contaminated	27
less contaminated	27
Method described by FAO (2014)	26
Community_P	24
Community_U	24
sand	18
na	18
World Reference Base for Soil Resources (WRB)	16
USDA web soil survey and soil taxonomy	16
Sedimentation	14
Organic Soil	8
NRCS Soil Survey Manual	7
websoilsurvey.sc.egov.usda.gov/App/WebSoilSurvey.aspx	6
Köhn, M. (1929). Korngrößenbestimmung mittels Pipettanalyse. Tonindustrie-Zeitung, 55:729–731. and Ad-Hoc-AG Boden (2005). Bodenkundliche Kartieranleitung 5 (KA5). Schweizerbart’sche Verlagsbuchhandlung, Stuttgart, 5 edition.	5

db.getCollection("biosample_set").find( { soil_type_meth : { $exists : true } } );

0

[ssarrafan]

Adding to current sprint per Mark. Need feedback from @mslarae13

[mslarae13]

@turbomam is it possible to export these in an excel file so I can look at them side by side?

[turbomam]

@mslarae13 you can copy markdown tables from GH issues and paste into Excel and they will look pretty good.

If I need to create some new tables for you, what is it that you want to see side by side?

[mslarae13]

Thanks Mark!

I didn't realize this would copy-paste so well.

"Soil taxonomy is a hierarchical soil classification system with six categories, or levels: order, suborder, great group, subgroup, family, and series. Soil taxonomy is a morphogenetic soil classification system using diagnostic horizons and features to infer pathways of soil genesis and formation." & "Soil taxonomy replaced the classification system in the US ... in 1938" - From this paper

Looking at these slots and what people have submitted, here's my conclusions.

1: FAO class is very specific. This should be an enumeration. Taxonomy (The FAO soil map was intended for mapping soils at a continental scale but not at local scale.)
2: local_class and soil_type look like classifications that may or may not be taxonomy.

Looking at GSC

slot	description	syntax
soil_type	Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.	"{termLabel} {[termID]}"
fao_class	Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups	enumeration
local_class	Soil classification based on local soil classification system	{text}

Local and soil type seem to be the same to me and soil type is more structured. I think we should drop local_class. This also allows for international taxonomy / classification since FAO an taxonomy are US specific
I have asked for feedback from ambassadors. I'll reach out to others in my network and report back with some additional thoughts on this before we make a final decision.

Adding to backlog until this is complete.

[ssarrafan]

Appears to be in progress based on recent comments. Moving to new sprint.

[ssarrafan]

No update this sprint. Removing from sprint. Backlog label was already added 2 weeks ago. Blocked on SubPort board.

[mslarae13]

Requirements to unblock:

• From this comment, link_class_info should be gone, but I still see it in the documentation.
  • Confirm, is it gone?
  • Deprecate it from NMDC documention
• Should we remove local_class
• Unclear from MIxS how local_class and soil_type are supposed to be different. Get clarification