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current land use enum with URL safe characters #972

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current land use enum with URL safe characters #972

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current land use enum with URL safe characters
turbomam May 27, 2025
fc973dc
no PV examples only is_as
turbomam Jun 2, 2025
9b697aa
Merge branch 'main' into 969-cur_land_use-was-an-enum-before-linkml
turbomam Jun 6, 2025
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109 changes: 94 additions & 15 deletions src/mixs/schema/mixs.yaml
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Expand Up @@ -25,6 +25,99 @@
nucleic acid sequence source:
investigation:
enums:
CurLandUseEnum:
permissible_values:
badlands:
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Can we add meanings to some of these PV's?

For example, is this an appropriate meaning for the badlands PV? http://purl.obolibrary.org/obo/ENVO_00000127

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This is a really good idea @sujaypatil96

@cmungall and I discussed it today. Chris suggested focusing our PV meaning efforts on

  1. enums where virtually all of the PVs would have a mapping to a well-maintained ontology
  2. slots that are already being frequently used in INSDC Biosamples

I don't think 2 is true here, and I think 1 might be very difficult to accomplish because the current land use PVs are a mixture of land uses (which might be in EnvO) and organisms that might be found on land being used in some way. The organism names are a mixture of singular and plural, and may have many to many mappings within NCBI taxonomy

So I am going to skip PV meaning sin the PR

cities:
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Similarly, meaning for cities – http://purl.obolibrary.org/obo/ENVO_00000856

conifers:
examples:
- value: cypress
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probably want to keep "conifers: pine"

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TIL the practice of adding examples on PV's! ✅

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I don't think PVs should ever have examples

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Will switch all examples to PVs of their own and assert is_a between them (hemlock) and their super-classes (conifer)

- value: fir
- value: pine
- value: spruce
crop trees:
examples:
- value: christmas trees
- value: fruit
- value: nursery trees
- value: nuts
farmstead:
gravel:
hardwoods:
examples:
- value: aspen
- value: elm
- value: hickory
- value: oak
hayland:
horticultural plants:
examples:
- value: tulips
industrial areas:
intermixed hardwood and conifers:
marshlands:
examples:
- value: grass
- value: rushes
- value: sedges
meadows:
examples:
- value: alfalfa
- value: bromegrass
- value: fescue
- value: grasses
- value: timothy
mines-quarries:
mudflats:
oil waste areas:
pastureland:
description: grasslands used for livestock grazing
permanent snow or ice:
rainforest:
description: evergreen forest receiving greater than 406 cm annual rainfall
rangeland:
roads-railroads:
rock:
row crops:
saline seeps:
salt flats:
sand:
shrub crops:
examples:
- value: blueberries
- value: filberts
- value: nursery ornamentals
shrub land:
examples:
- value: creosote bush
- value: eucalyptus
- value: mesquite
- value: sage-brush
- value: shrub oak
small grains:
successional shrub land:
examples:
- value: blackberries
- value: chokecherry
- value: hazels
- value: shrub dogwoods
- value: sumacs
- value: tree saplings
swamp:
description: permanent or semi-permanent water body dominated by woody plants
tropical:
examples:
- value: mangrove
- value: palms
tundra:
examples:
- value: lichens
- value: mosses
vegetable crops:
vine crops:
examples:
- value: grapes

BiolStatEnum:
permissible_values:
breeder's line:
Expand Down Expand Up @@ -5658,28 +5751,14 @@
slot_uri: MIXS:0001119
multivalued: true
cur_land_use:
annotations:
Expected_value: enumeration
description: Present state of sample site
title: current land use
examples:
- value: conifers
keywords:
- land
- use
string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt
flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small
grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands
(grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands
used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub
land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional
shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub
crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers
(e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed
hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest
receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water
body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery
trees)]'
range: CurLandUseEnum
slot_uri: MIXS:0001080
cur_vegetation:
annotations:
Expand Down