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…add method (incomplete)
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What is the MIxS policy on deprecation? I would not delete this as you have done in the PR. Instead
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cmungall
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cmungall
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deprecate instead of delete
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Discuss with CIG In short |
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When this extension was created, They wanted to specify that it was the water, as they pump water into the line and take the sample of the water, to examine microbes before extracting the oil. I would not deprecate this term. It is specific to their use case.LynnSent from my iPhoneOn Jul 17, 2024, at 6:31 PM, Montana ***@***.***> wrote:
Discuss with CIG
IF there is need for HCR extensions to specify the tot_c content of the WATER vs the sample, we should update the description to emphasize that the water is NOT the same. And the tot_nitro_content should be used for the water extensions as in this case it is the sample.
In short
Is this slot describing a property of the SAMPLE or a some aspect of the ENVIRONMENT in which the sample was collected
See : #664 (comment)
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Thanks @lschriml I realized that from a comment from @cmungall |
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Sounds good. For the hydrocarbon work, they are drilling for oil. After they drill they pump in water, and sample it for microbes.Interestingly, this standard is used across the drill industry.Cheers,LynnSent from my iPhoneOn Jul 19, 2024, at 6:29 PM, Montana ***@***.***> wrote:
Thanks @lschriml
I realized that from a comment from @cmungall
With that, I agree we could probably close this PR and issue, but we should visit the included discussion to make sure we're providing clear text on when these data as metadata values are about the "sample or a some aspect of the environemnt in which the sample was collected"
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This is a great discussion about user requirements and GSC/MIxS policies, esp. with respect to the LinkML deprecation procedure that has been approved by the TWG. For me the key issue here is the effort that goes into creating MIxS terms and Checklists/Extensions in support of specific users from specific domains, versus the ongoing effort that goes into managing MIxS as a whole. @mslarae13 has opened a lot of thoughtful issues and PRs about what appear to be redundant terms. Whether they are merged with changes or just closed, the general theme shouldn't be neglected. Folklore-like reflection on the history of a term can be a great addition to a GitHub ticket like this, but it shouldn't be necessary. At a minimum the descriptions of the two terms (or comments?) should be updated with clear differentiating language. Moving forward, all of this knowledge should be captured in a rolling format that is easy to integrate with the LinkML representation of MIxS. |
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On the next CIG/TWG calls, let's start to put the process into place, to
ensure we are identifying the suggested changes,
into the GSC workflow.
To ensure we do not lose the domain experts knowledge that was used to
create the standards, while taking advantage of new information to
improve MIxS.
*To be clear: *we will not be changing terms/definition content, without
the process of including the domain expert teams.
All suggestions for alternative definitions
(descriptions) should go through this process, to ensure the integrity of
the information.
None of us are experts in all areas, and we have found
that working directly with the domain experts is the best path forward.
Cheers,
Lynn
…On Mon, Jul 22, 2024 at 11:02 AM Mark Andrew Miller < ***@***.***> wrote:
This is a great discussion about user requirements and GSC/MIxS policies,
esp. with respect to the LinkML deprecation procedure that has been
approved by the TWG.
For me the key issue here is the effort that goes into creating MIxS terms
and Checklists/Extensions in support of specific users from specific
domains, *versus* the ongoing effort that goes into managing MIxS as a
whole. @mslarae13 <https://github.com/mslarae13> has opened a lot of
thoughtful issues and PRs on this topic, and whether they are merged with
changes or just closed, the general theme shouldn't be neglected.
Folklore-like reflection on the history of a term can be a great addition
to a GitHub ticket like this, but it shouldn't be necessary. At a minimum
the descriptions of the two terms (or comments?) should be updated with
clear differentiating language. Moving forward, all of this knowledge
should be captured in a rolling format that is easy to integrate with the
LinkML representation of MIxS.
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Reply to this email directly, view it on GitHub
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You are receiving this because you were mentioned.Message ID:
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--
Lynn M. Schriml, Ph.D.
Associate Professor
Institute for Genome Sciences
University of Maryland School of Medicine
Department of Epidemiology and Public Health
670 W. Baltimore St., HSFIII, Room 3061
Baltimore, MD 21201
P: 410-706-6776 | F: 410-706-6756
***@***.***
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lschriml
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5-TechnicalUpdates
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Pull request overview
Deprecates the water-specific total nitrogen slot and updates affected extensions to use tot_nitro_content (and associated method slot) instead, addressing #680’s concern about environment-specific term definitions in the MIxS schema.
Changes:
- Removed the
tot_nitroslot definition (MIXS:0000102) from the schema. - Replaced
tot_nitrowithtot_nitro_content(and addedtot_nitro_cont_meth) in several extensions’ slot lists. - Added
tot_nitro_cont_methto additional extensions beyond those listed in the PR description.
Comments suppressed due to low confidence (2)
src/mixs/schema/mixs.yaml:14366
- This change removes the
tot_nitroslot (MIXS:0000102) entirely rather than deprecating it. If downstream users still providetot_nitroin data, this becomes a breaking schema change; consider keeping the slot withdeprecated: true(and a clear replacement pointer totot_nitro_content) instead of deleting it outright.
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
tot_nitro_cont_meth:
description: Reference or method used in determining the total nitrogen
title: total nitrogen content method
examples:
src/mixs/schema/mixs.yaml:14380
- After removing
tot_nitrofrom the source schema, the committed generated artifacts (e.g., the Python datamodel) will be out of sync unless regenerated; the repo Makefile includes agen-projectstep that outputssrc/*/datamodel/*py. Please regenerate and commit the updated datamodel so it no longer exposestot_nitroif the slot is truly being removed/deprecated.
tot_nitro_cont_meth:
description: Reference or method used in determining the total nitrogen
title: total nitrogen content method
examples:
- value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00
keywords:
- content
- method
- nitrogen
- total
slot_uri: MIXS:0000338
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
tot_nitro_content:
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| - tot_diss_nitro | ||
| - tot_inorg_nitro | ||
| - tot_nitro | ||
| - tot_nitro_content |
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In the Water extension, replacing tot_nitro (concentration) with tot_nitro_content (content) changes the meaning of the field and likely the expected units. If the intent is to make total nitrogen applicable beyond water, consider generalizing the existing concentration slot (MIXS:0000102) and deprecating/aliasing names, rather than switching to a different “content” slot.
| - tot_nitro_content | |
| - tot_nitro |
| - temp | ||
| - tot_carb | ||
| - tot_nitro_content | ||
| - tot_nitro_cont_meth | ||
| - tot_org_carb |
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The PR description lists updates for HydrocarbonResources* / Water / WastewaterSludge, but this diff also adds tot_nitro_cont_meth to the MicrobialMatBiofilm extension. Please either update the PR description/scope to include this extension or revert this additional change if it’s unintended.
| @@ -19742,6 +19722,7 @@ classes: | |||
| - tot_carb | |||
| - tot_depth_water_col | |||
| - tot_nitro_content | |||
| - tot_nitro_cont_meth | |||
| - tot_org_carb | |||
| - turbidity | |||
| - nitrite | ||
| - ammonium | ||
| - tot_nitro | ||
| - tot_nitro_content |
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tot_nitro_content is defined as “Total nitrogen content of the sample” (mass per mass examples), whereas the removed tot_nitro term was explicitly a concentration term (mass per volume) with water-oriented preferred units. Swapping tot_nitro → tot_nitro_content in this extension changes the semantics/expected units; consider instead generalizing tot_nitro’s description (removing the water-specific wording) or introducing a new generalized concentration term rather than reusing a “content” slot.
| - tot_nitro_content | |
| - tot_nitro |
| - nitrite | ||
| - ammonium | ||
| - tot_nitro | ||
| - tot_nitro_content |
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tot_nitro_content is a “content” slot (not a concentration slot), so replacing tot_nitro with tot_nitro_content here may change the intended measurement units/meaning for this extension. If the goal is only to remove water-specific wording, consider updating/retaining the concentration slot (MIXS:0000102) as deprecated/renamed rather than switching to tot_nitro_content.
| - tot_nitro_content | |
| - tot_nitro |
| - tot_nitro_content | ||
| - tot_nitro_cont_meth |
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tot_nitro (removed) was a concentration term for water samples, while tot_nitro_content is defined as a sample “content” term. Replacing it in WastewaterSludge likely changes semantics/expected units; consider keeping a concentration-oriented slot (or adding a new generalized one) instead of mapping to the “content” slot.
| - tot_nitro_content | |
| - tot_nitro_cont_meth | |
| - tot_nitro | |
| - tot_nitro_meth |
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Fixes #680
tot_nitro=Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
domain_of:
tot_nitro_content=Total nitrogen content of the sample
domain_of:
tot_nitro&tot_nitro_contentare the same, with the exception thattot_nitrois water specific in its descriptionIn this PR,
tot_nitrofor deprecationtot_nitroit used to now usetot_nitro_content