meadow biome

[pbuttigieg]

I'm not sure any biome classification schemes include meadows. this is more an ecosystem-level class

one can have meadows in multiple biomes

[pbuttigieg]

I can't find any way to render this a biome- a meadow is like a clearing, it can occur in many biomes

@turbomam this can be rendered as a ecosystem class.

[turbomam]

I can't find any way to render this a biome- a meadow is like a clearing, it can occur in many biomes

@turbomam this can be rendered as a ecosystem class.

Thanks @pbuttigieg . You comments make sense.

We are trying to instantiate NMDC Biosamples, which must be annotated with the triad of MIxS environmental context terms.

I believe we have a data provider with a field whose semantics are similar to env_broad_scale. In some circumstances that field id populated with the word "meadow". We are trying to stick to the guidance that when EnvO classes are used for env_broad_scale, they should be subclasses of Biome.

@aclum might be able to say more about this.

It looks like the source of the Biosamples is https://gold.jgi.doe.gov/study?id=Gs0135149 and the string "meadow" comes from the Ecosystem Subtype part of the GOLD "ECOSYSTEM CLASSIFICATION"

Here's an example GOLD Biosample: https://gold.jgi.doe.gov/biosample?id=Gb0191659

And an example NMDC Biosample, form the same study: https://data.microbiomedata.org/details/sample/igsn:IEWFS0010

Maybe 'meadow ecosystem' could be the env_local_scale and we could use 'terrestrial biome' as the env_broad_scale

[pbuttigieg]

https://link.springer.com/article/10.1007/s00477-022-02327-7#Sec2

this study site was quite broad, but

2.1.2 Climate and biome zones

The East River watershed area is defined as having a continental, subarctic climate with long, cold winters and short, cool summers. Excursions in river discharge are driven primarily by snowmelt in late spring to early summer, with mid‐ to late‐summer monsoonal rainfall inducing rapid but punctuated increases in flow. The watershed comprises several biome zones–montane, subalpine, and alpine life zones, which collectively include aspen, meadow, mixed conifer, sagebrush, willow, grasses, sedges, and a diversity of forbs. The area is characterized by variable climatic conditions across the drainage watersheds, with quite variable rainfall and temperature. The watershed has a mean annual temperature of ∼0 °C, with average minimum and maximum temperatures of − 9.2 and 9.8 °C, respectively; winter and growing seasons are distinct and greatly influence the hydrology and biogeochemistry of the watershed. An average precipitation is 1200 mm yr−1, the majority of which falls as snow, which is typical for the Upper Colorado River Basin. A typical feature of the East River watershed is that air reaches the mountains, and then moves up the windward side of a mountain and cools. As a result, humidity increases and orographic clouds and precipitation can develop.

so you're likely looking for one or more of

http://purl.obolibrary.org/obo/ENVO_01001836 or its subclasses

http://purl.obolibrary.org/obo/ENVO_01001837

http://purl.obolibrary.org/obo/ENVO_01001835 or its subclasses

[aclum]

FWIW GOLD has 'grassland biome [ENVO_01000177]' as env_broad scale and meadow ecosystem [ENVO_00000108] as env_local_scale

[pbuttigieg]

I think stating that this site is alpine/subalpine/montane (you'll have to delve a little to figure out if the samples came from all three ) is more informative than the grassland biome, as "meadow" gets you much of that.

However, one can add an array of ontology terms in MIxS records, I think

[turbomam]

Thanks, that's helpful feedback

[pbuttigieg]

@turbomam so what will we do with this PR? Do you need a new meadow class?

[turbomam]

@turbomam so what will we do with this PR? Do you need a new meadow class?

I'm currently making a proposal to NMDC with alternative EnvO terms for the MIxS environmental context fields

I don't think we will need this term

I'll write back later today