Montana

Add deprecation documentation to github docs

1

For https://genomicsstandardsconsortium.github.io/mixs/ We should add a page about the deprecation. - what it is - why we're doing it - how it's done - how to find deprecated terms Like...

make URL for deprecation.yaml id

1

I added a fake URL ID for deprecation.yaml. "LinkML doesn't do "link checking" of the URLs in id slots or wherever else so technically you would be okay putting in...

term total nitrogen concentration (tot_nitro) is water specific, should be general

6

**Describe the bug** A clear and concise description of what the bug is. The description of tot_nitro is : Total nitrogen concentration of **water samples**, calculated by: total nitrogen =...

slot link_climate_info has no guidance or examples. criteria for completion - [ ] identify how the slot has been used (if at all) in the past, @turbomam provide a query...

slot soil_texture_meth has no guidance or examples.. & soil_text_measure does not have examples. criteria for completion - [ ] identify how the slots have been used (if at all) in...

`heavy_metals` description and guidance is not LinkML compliant

1

https://genomicsstandardsconsortium.github.io/mixs/0000652/ Current: ``` heavy_metals: annotations: Expected_value: heavy metal name;measurement value unit Preferred_unit: microgram per gram description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals...

**Current term details** Please supply the current details of the term that you would like to update: ``` Term name - "air temperature regimen", "biotic regimen", "chemical administration", "gaseous environment",...

water_content & water_content_meth

3

**Current term details** Please supply the current details of the term that you would like to update: ``` Term name - water_content & water_cont_soil_meth Term ID - [if known] Structured...

Add pH method to sediment

1

**Current term details** Please supply the current details of the term that you would like to update: ``` Term name - pH method Term ID - pH_meth Structured comment name...

**Current term details** Please supply the current details of the term that you would like to update: ``` Term name - store_cond, samp_stor_dur, samp_stor_loc, samp_store_temp Term ID - [if known]...