Determine if and how climate_environment will be used in the submission schema

[mslarae13]

I am not sure how to write this example according to the structure. Would like to see some completed examples

Completion

• Provide Montana an export from NCBI of metadata records that included this field and how they wrote it (@turbomam )
• Provide Montana some examples of how it SHOULD be written
• Update NMDC schema with examples (Montana)
• Incorporate change into submission portal (Mark & kitware)

[turbomam]

I do think I can check off most of those boxes within a day or two into next week

[turbomam]

GSC's MIxS Specification

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

Environmental package	agriculture	plant-associated
Structured comment name	climate_environment	climate_environment
Package item	climate environment	climate environment
Definition	Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates	Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
Expected value	climate name;treatment duration;interval;experimental duration	climate name;treatment interval and duration
Value syntax	{text};{period};{interval};{period}	{text};{Rn/start_time/end_time/duration}
Example		tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
Requirement	C	X
Preferred unit
Occurrence	m	m
MIXS ID	MIXS:0001040	MIXS:0001040

BBOP relational version of NCBI biosample_set:

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

value	count
Mediterranean, subtropical	4120
not applicable	1283
NA	763
not collected	482
Humid subtropical	392
Lab microcosm	192
greenhouse	113
Warm temperate (Cfb)	95
Boreal (Dfb)	88
control conditions	40
controlled conditions, branch partially covered by plastic bag	36
freeze-thaw	35
continental with Mediterranean influences	27
Humid continental climate	25
subalpine	24
riparian zone	23
controlled conditions	18
freeze	17
thaw	17
submediterranean	14
drought	14
Controlled	12
tropical wet and dry climate	12
cold	8
heat	8
missing	7
Tropical	7
2 weeks cold storage	6
Dry	6
3 weeks cold storage	6
4 weeks cold storage	6
5 weeks cold storage	6
Orchard at harvest	6
Agricultural environment	6
Dry, Hot	5
Temperate	5
Common Garden, Flooding	3
Common Garden, Control	3
Common Garden, Drougth	3
Greenhouse, Heat, CO2	3
https://kare.ucanr.edu/Weather_Physical_-_Biological_Data/	3
Greenhouse, Drought, Heat, CO2	3
Greenhouse, Flooding, Heat	3
temperate climate	3
Greenhouse, Drought, Heat	3
Greenhouse, Heat	3
Greenhouse, Flooding, Heat, CO2	3
common garden setup	2
KG biological replicates 3	2
KG biological replicates 1	2
ambient conditions	2
S biological replicates 2	2
desertic	2
CK biological replicates 3	2
KG biological replicates 2	2
watered	2
S biological replicates 1	2
none	2
Not applicable	2
S biological replicates 3	2
CK biological replicates 2	2
CK biological replicates 1	2

[turbomam]

Any Biosamples with a climate_environment value in the current NMDC production MongoDB?

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

0

[ssarrafan]

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

[mslarae13]

@turbomam the NCBI examples are quite variable, and not what I'd expect. I am not surprised there's no time or duration for climate manipulation, but rather people just describe the comment.

I think , considering the examples we have, this field should just be a way to describe the climate_environment. and not as a "duration of treatment"

So from the plant example "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" would just be "tropical climate"

@turbomam thoughts?

[turbomam]

@mslarae13 That's fine with me. Do you want to allow any string, or would you like to have a validation pattern, or some enumerated values?

[ssarrafan]

Discussion seems to be ongoing, moving to new sprint

[mslarae13]

Name is misleading and should be climate treatment... People are putting biome and other information that should be in a different column here... Ramona suggests deprecating this term. I will put an issue into GSC

[ramonawalls]

Nearly all of the values in this slot are wrong and should go into one of the ENVO slots (e.g., biome). There is a legitimate need to record information about experimental environmental conditions, but there are either existing slots for that information or we should add new one(s) that are less confusing.

I recommend deprecating this term in MIxS and replacing it mostly with existing terms. If there is some environmental data that can't be captured, we can create new terms that are clearer.

[mslarae13]

GenomicsStandardsConsortium/mixs#591

[mslarae13]

@turbomam
Should we remove this from NMDC now? Or wait for GSC update?

Also, we pulled this term into the soil package. It can go away. (GSC only has it in agriculture & plant)

@pkalita-lbl FYI

[turbomam]

I'll remove in 7.6.1

[mslarae13]

@turbomam did this get completed?

[mslarae13]

Decision: Will deprecate this term.
@sierra-moxon has created a deprecation protocol for NMDC. We'll discuss implementing this in to GSC & will deprecate this term when ready.