Minor metadata edits 2023 10 (#781)

* Update Cheesman_2020 basis_of_record field

* recode `entity_context` as `method_context` for some datasets

* fixes based on running all dataset tests

data/ABRS_2023/metadata.yml

@@ -94,7 +94,6 @@ dataset:
   taxon_name: taxon_name
   trait_name: trait_name
   value: trait_value
-  value_type: value_type
   measurement_remarks: measurement_remarks
   description: Plant growth form data extracted from the Flora of Australia online
     website.
@@ -138,7 +137,7 @@ contexts:
   - value: inferred_from_taxonomy
     description: Trait value inferred from a higher level taxon description.
 - context_property: entity_measured
-  category: entity_context
+  category: method_context
   var_in: entity_measured
 - context_property: replicate observations
   category: temporal_context
@@ -148,6 +147,7 @@ traits:
   unit_in: .na
   trait_name: fruit_colour
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: When specified in the taxon description, only the colours of the fruit
@@ -157,6 +157,7 @@ traits:
   unit_in: .na
   trait_name: fruit_dehiscence
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as dehiscent from a variety of terms in the text including
@@ -165,6 +166,7 @@ traits:
   unit_in: .na
   trait_name: fruit_type
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing a fruit type based on the presence of terms
@@ -173,6 +175,7 @@ traits:
   unit_in: .na
   trait_name: root_system_type
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as "taproot_present taproot_not_present" if the taproot
@@ -181,6 +184,7 @@ traits:
   unit_in: .na
   trait_name: storage_organ
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing these storage organs if mentioned in the
@@ -189,6 +193,7 @@ traits:
   unit_in: .na
   trait_name: seed_shape
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: There were a wide variety of terms used to describe seed shapes across
@@ -198,6 +203,7 @@ traits:
   unit_in: .na
   trait_name: seed_surface_reflectivity
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as as reflective if described as shiny or reflective in
@@ -206,6 +212,7 @@ traits:
   unit_in: .na
   trait_name: seed_surface_hairs
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing seed hairs if any portion of the seed surface
@@ -214,6 +221,7 @@ traits:
   unit_in: .na
   trait_name: seed_surface_texture
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: There were a wide variety of terms used to describe seed textures across
@@ -223,6 +231,7 @@ traits:
   unit_in: .na
   trait_name: leaf_compoundness
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Leaves of taxa were scored as simple or compound from the presence of these
@@ -232,6 +241,7 @@ traits:
   unit_in: .na
   trait_name: leaf_glaucousness
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as "glaucous non_glaucous" if the word "glaucous" described
@@ -240,6 +250,7 @@ traits:
   unit_in: .na
   trait_name: leaf_lobation
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing lobed leaves from mentions of leaf lobes
@@ -250,6 +261,7 @@ traits:
   unit_in: .na
   trait_name: leaf_pendulousness
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as "pendulous not_pendulous" if two leaf states were mentioned
@@ -258,6 +270,7 @@ traits:
   unit_in: .na
   trait_name: leaf_arrangement
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing a particular leaf arrangement if mentioned
@@ -267,6 +280,7 @@ traits:
   unit_in: .na
   trait_name: leaf_base_shape
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing leaf base shapes when taxon descriptions
@@ -276,6 +290,7 @@ traits:
   unit_in: .na
   trait_name: leaf_margin
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Taxa were scored as possessing teeth on the margins of leaves from the
@@ -285,6 +300,7 @@ traits:
   unit_in: .na
   trait_name: leaf_phyllotaxis
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Leaves of taxa were scored as opposite, alternate or whorled from the presence
@@ -294,6 +310,7 @@ traits:
   unit_in: .na
   trait_name: leaf_shape
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: There were a wide variety of terms used to describe leaf shapes across
@@ -304,6 +321,7 @@ traits:
   unit_in: .na
   trait_name: stem_growth_habit
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: Stem growth habit includes terms to describe a plant's three-dimensional
@@ -312,6 +330,7 @@ traits:
   unit_in: mm
   trait_name: fruit_length
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: The term used to describe the fruit length was stored as a measurement
@@ -321,6 +340,7 @@ traits:
   unit_in: mm
   trait_name: fruit_width
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: The term used to describe the fruit width was stored as a measurement remark
@@ -330,6 +350,7 @@ traits:
   unit_in: mm
   trait_name: fruit_height
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: The term used to describe the fruit breadth or thickness was stored as
@@ -340,6 +361,7 @@ traits:
   unit_in: mm
   trait_name: leaf_length
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: The term used to describe the length of the leaf or leaf analogue was stored
@@ -348,6 +370,7 @@ traits:
   unit_in: mm
   trait_name: leaf_width
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: The term used to describe the width of the leaf or leaf analogue was stored
@@ -356,20 +379,23 @@ traits:
   unit_in: mm
   trait_name: petiole_length
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: This data records the length of the petiole as recorded in the taxon description.
 - var_in: petiole_width
   unit_in: mm
   trait_name: petiole_width
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: This data records the width of the petiole as recorded in the taxon description.
 - var_in: seed_length
   unit_in: mm
   trait_name: seed_length
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: This data records seed length as described in the taxon description. Seeds
@@ -379,6 +405,7 @@ traits:
   unit_in: mm
   trait_name: seed_width
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: This data records the seed width as described in the text. Seeds which
@@ -388,6 +415,7 @@ traits:
   unit_in: mm
   trait_name: seed_height
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: This data records the seed breadth as described in the text. Seeds which
@@ -397,13 +425,15 @@ traits:
   unit_in: mm
   trait_name: plant_height
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: Maximum plant vegetative height of a mature individual.
 - var_in: plant_photosynthetic_organ
   unit_in: .na
   trait_name: plant_photosynthetic_organ
   entity_type: species
+  value_type: value_type
   basis_of_value: expert_score
   replicates: .na
   methods: The dominant photosynthetic organ was scored as leaf, phyllode or cladode
@@ -414,6 +444,7 @@ traits:
   unit_in: mm
   trait_name: leaf_lamina_posture
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: Taxa were scored as possessing a leaf lamina posture if a descriptor of
@@ -423,6 +454,7 @@ traits:
   unit_in: mm
   trait_name: leaf_margin_posture
   entity_type: species
+  value_type: value_type
   basis_of_value: measurement
   replicates: .na
   methods: Taxa were scored as possessing a leaf margin posture if the word "margin"

data/Cheesman_2020/metadata.yml

@@ -45,7 +45,7 @@ dataset:
     in combination, reflect canopy position of leaves within a modern closed canopy
     forest, with the goal of understanding how these data could be applied to the
     fossil record.
-  basis_of_record: field field_experiment
+  basis_of_record: basis_of_record
   life_stage: adult
   sampling_strategy: All leaf samples were obtained from the Daintree Rainforest Observatory
     (DRO), located in Cape Tribulation (-16.117 N, 145.45 E), 140 kilometres north

data/Cowling_1987/metadata.yml

@@ -69,8 +69,6 @@ contexts:
   category: temporal_context
   var_in: cone_age
   values:
-  - value: .na.real
-    description: .na.character
   - value: all ages
     description: Value across all cone ages.
   - value: '2'
@@ -280,7 +278,7 @@ traits:
     the start of the wet season when conditions are approaching optimal for germination
     and establishment (Cowling & Lamont 1987)'
 substitutions:
-- trait_name: bud_bank_location
+- trait_name: .na
   find: lignotuber
   replace: basal_stem_buds
 taxonomic_updates: .na