fao_class description has link to a dead site

[mslarae13]

Describe the bug A clear and concise description of what the bug is. the link provided to complete fao_class is broken (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 behavior A clear and concise description of what you expected to happen.

The link should work, or we should provide a new link.

Additional context Add any other context about the problem here.

Some things to consider... how often is this slot used? Does an updated link exist? Is this the same thing-> https://www.britannica.com/science/soil/FAO-soil-groups (i don't know what the previous site link looked like)

[mslarae13]

@turbomam could you query NCBI and see how/ if this slot is filled out much?

[only1chunts]

looking at the FAO website and following links on there, it seems like they now use/recommend ISRIC world soil information list found here: https://www.isric.org/explore/world-soil-distribution I'm not sure if we should be using that list instead, or if we should be creating an enum ourselves (based on that list and linking to matching ontology terms - the few I checked are in ENVO already).

[turbomam]

select
    "value",
    count(1)
from
    all_attribs aa
where
    attribute_name = 'fao_class'
group by
    "value"
order by
    count(1) desc ;

There were only 6242 NCBI Biosamples with a fao_class annotation as of July.

value	count
Luvisols	1046
not applicable	452
not collected	431
rendzina	368
Typic Hapludalfs	270
Oxisol	253
Mollisol	232
using EC meter (HORIBA) with a 2:5 soil/water suspension	192
Endostagnic Luvisol from glacial till	192
NA	169
Hoytville silty clay loam	133
Kokomo silty clay loam	132
Phaeozem	126
Fluvisol	120
cambisol	101
chernozem	100
Greyzemic Phaeozem Albic	97
"Fine-silty, mixed, thermic Oxyaquic Fragiudalfs"	96
Chernozem	90
"Fine, mixed, active, mesic Typic Paleudalfs"	90
mesic Lamellic Hapludalfs	90
Typic Argiudoll	88
Cambisol	83
loess	80
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 1:10 soil/water suspension (mS cm-1)	78
Vitric eutric epiarenic	72
missing	67
Typic Argiudolls	66
Podzol	59
Andosol	56
Luvic Phaeozem	54
Luvisol	51
Nitisol	51
Arenosol	48
"Fine-loamy, mixed, subactive, thermic typic Hapludults"	47
Calcaric, Eutric Fluvisol	36
Umbric Epistagnic Albeluvisol	36
Gleysol	34
Cryosol	31
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 1:5 soil/water suspension	30
3a	30
Histosol	27
Haplic Phaeozem	27
Pellic Vertisol	27
arenosols	24
Leptosol	23
sod-podzolic	22
Earth-cumuli-Orthic Anthrosols	21
using EC meter (LAQUAtwin EC-33B, HORIBA) with a 2:5 soil/water suspension (mS cm-1)	20
na	19
Calcisols	18
Ferralsol	17
Mottled Fragic Pallic Soil (Ustochrept)	16
Regosol	12
Vertisol	12
Oxisols	12
Phaozem	9
Planosol	8
Haplic Luvisol	6
Geric Ferralsol	5
Stagnic Cambisol	4
Lithosol	3
Cambisol (almost Ferralsol)	3
fluvisol	3
histosol	3
Kastanozem	3
Umbrisol	3
loamy-skeletal, mixed, active, mesic Lithic Dystrudept	3
vertisol	2
ferralsols	2
phaeozem	2
gypsisol	2
xerosol	1
krasnozem	1
O-horizon	1
fao_class	1
Dark Chestnut soil	1
A - Non-calcaric lithosol, B -D - Typical podzolic brown soil, E - Saline alluvial gley soil	1
Alisol	1

[mslarae13]

A good chunk of what is in NCBI currently is some variation of the FAO classification.. variations in plurality and capitalization, but it's one of the closer ones I've seen!

That said, I agree with @only1chunts. We should create an FAO enumeration and require it be one of the provided list. Thanks for the link Chris, I wasn't able to find that site.

I'll work on the enum and making the updates to the description now.

[mslarae13]

Updated, see https://github.com/GenomicsStandardsConsortium/mixs/pull/726

Note, the enum already existed so I just updated the available values