overwrote some TODO descriptions for #231 #239
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wdduncan
suggested changes
Jan 12, 2022
src/schema/nmdc.yaml
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| @@ -796,27 +796,27 @@ slots: | |||
| ecosystem: | |||
| is_a: gold_path_field | |||
| description: >- | |||
| TODO | |||
| An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. See GOLD terminology at https://gold.jgi.doe.gov/help. | |||
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I think this and the other GOLD path descriptions can be shortened. For example, the ecosystem description can be shorted to:
An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment.
Having the shortened description will help if we want the description to show in tooltips.
The rest of the information is good. But, I would put the following in a comment
That is, I would put the following in a comment:
The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. See GOLD terminology at https://gold.jgi.doe.gov/help.
@cmungall may have different opinion though.
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Good point
For some of the Gold Ecosystem Classification Levels, I don't think the first sentence alone provides enough description. But I have moves the examples into comments
For example I don't find
Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes
informative at all.
I have added a statement like
Ecosystem type is in position 3/5 in a GOLD path.
to each of the descriptions.
|
@turbomam Please update the changelog. |
|
Ideally we would have an enum for each path component, but for now just
listing a few key examples would go a long way to elucidating these
…On Fri, Jan 14, 2022 at 6:38 AM Mark A. Miller ***@***.***> wrote:
***@***.**** commented on this pull request.
------------------------------
In src/schema/nmdc.yaml
<#239 (comment)>
:
> @@ -796,27 +796,27 @@ slots:
ecosystem:
is_a: gold_path_field
description: >-
- TODO
+ An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. See GOLD terminology at https://gold.jgi.doe.gov/help.
Good point
For some of the Gold Ecosystem Classification Levels, I don't think the
first sentence alone provides enough description. But I have moves the
examples into comments
For example I don't find
Ecosystem subtypes represent further subdivision of Ecosystem types into
more distinct subtypes
informative at all.
I have added a statement like
Ecosystem type is in position 3/5 in a GOLD path.
to each of the descriptions.
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wdduncan
reviewed
Jan 14, 2022
|
|
||
| ecosystem_category: | ||
| is_a: gold_path_field | ||
| description: >- | ||
| TODO | ||
| Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path. | ||
| comments: The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. |
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it should. The schemaloader is liberal in what it accepts, and will convert single value to list for list types. Nevertheless we should conform.
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overwrote some TODO descriptions for #231
definitions provided by https://gold.jgi.doe.gov/help via @emileyfadrosh