From ed8dde7cd6bee1fedc07220df868a236b4871abd Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Fri, 3 Nov 2023 19:25:06 +1100 Subject: [PATCH] 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 | 36 +++++++++++++++++++++++++++++++-- data/Cheesman_2020/metadata.yml | 2 +- data/Cowling_1987/metadata.yml | 4 +--- data/NHNSW_2023/metadata.yml | 36 +++++++++++++++++++++++++++++++-- data/NTH_2023/metadata.yml | 36 +++++++++++++++++++++++++++++++-- data/RBGV_2023/metadata.yml | 36 +++++++++++++++++++++++++++++++-- data/SAH_2023/metadata.yml | 36 +++++++++++++++++++++++++++++++-- data/Tsakalos_2020/metadata.yml | 2 +- data/WAH_2023_1/metadata.yml | 36 +++++++++++++++++++++++++++++++-- data/WAH_2023_2/metadata.yml | 36 +++++++++++++++++++++++++++++++-- 10 files changed, 241 insertions(+), 19 deletions(-) diff --git a/data/ABRS_2023/metadata.yml b/data/ABRS_2023/metadata.yml index c4816dc64..2c1b6cfc9 100644 --- a/data/ABRS_2023/metadata.yml +++ b/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 @@ -356,6 +379,7 @@ 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. @@ -363,6 +387,7 @@ traits: 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. @@ -370,6 +395,7 @@ traits: 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 @@ -397,6 +425,7 @@ 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. @@ -404,6 +433,7 @@ traits: 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" diff --git a/data/Cheesman_2020/metadata.yml b/data/Cheesman_2020/metadata.yml index 696de1754..f6975ce34 100644 --- a/data/Cheesman_2020/metadata.yml +++ b/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 diff --git a/data/Cowling_1987/metadata.yml b/data/Cowling_1987/metadata.yml index 93fb025b7..c5c57fce0 100644 --- a/data/Cowling_1987/metadata.yml +++ b/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 diff --git a/data/NHNSW_2023/metadata.yml b/data/NHNSW_2023/metadata.yml index 0fc7f4777..b9821575c 100644 --- a/data/NHNSW_2023/metadata.yml +++ b/data/NHNSW_2023/metadata.yml @@ -104,7 +104,6 @@ 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 NT Flora Online basis_of_record: literature @@ -146,7 +145,7 @@ 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 @@ -156,6 +155,7 @@ 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 @@ -165,6 +165,7 @@ 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 @@ -173,6 +174,7 @@ 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 @@ -181,6 +183,7 @@ 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 @@ -189,6 +192,7 @@ 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 @@ -197,6 +201,7 @@ 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 @@ -206,6 +211,7 @@ 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 @@ -214,6 +220,7 @@ 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 @@ -222,6 +229,7 @@ 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 @@ -231,6 +239,7 @@ 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 @@ -240,6 +249,7 @@ 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 @@ -248,6 +258,7 @@ 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 @@ -258,6 +269,7 @@ 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 @@ -266,6 +278,7 @@ 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 @@ -275,6 +288,7 @@ 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 @@ -284,6 +298,7 @@ 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 @@ -293,6 +308,7 @@ 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 @@ -302,6 +318,7 @@ 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 @@ -312,6 +329,7 @@ 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 @@ -320,6 +338,7 @@ 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 @@ -329,6 +348,7 @@ 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 @@ -338,6 +358,7 @@ 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 @@ -348,6 +369,7 @@ 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 @@ -356,6 +378,7 @@ 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 @@ -364,6 +387,7 @@ 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. @@ -371,6 +395,7 @@ traits: 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. @@ -378,6 +403,7 @@ traits: 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 @@ -387,6 +413,7 @@ 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 @@ -396,6 +423,7 @@ 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 @@ -405,6 +433,7 @@ 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. @@ -412,6 +441,7 @@ traits: 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 @@ -422,6 +452,7 @@ 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 @@ -431,6 +462,7 @@ 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" diff --git a/data/NTH_2023/metadata.yml b/data/NTH_2023/metadata.yml index 61b85e06a..cfc444c78 100644 --- a/data/NTH_2023/metadata.yml +++ b/data/NTH_2023/metadata.yml @@ -95,7 +95,6 @@ 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 NT Flora Online basis_of_record: literature @@ -137,13 +136,14 @@ contexts: category: temporal_context var_in: observation_number - context_property: entity measured - category: entity_context + category: method_context var_in: entity_measured traits: - var_in: fruit_colour 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 @@ -153,6 +153,7 @@ 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 @@ -161,6 +162,7 @@ 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 @@ -169,6 +171,7 @@ 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 @@ -177,6 +180,7 @@ 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 @@ -185,6 +189,7 @@ 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 @@ -194,6 +199,7 @@ 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 @@ -202,6 +208,7 @@ 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 @@ -210,6 +217,7 @@ 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 @@ -219,6 +227,7 @@ 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 @@ -228,6 +237,7 @@ 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 @@ -236,6 +246,7 @@ 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 @@ -246,6 +257,7 @@ 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 @@ -254,6 +266,7 @@ 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 @@ -263,6 +276,7 @@ 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 @@ -272,6 +286,7 @@ 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 @@ -281,6 +296,7 @@ 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 @@ -290,6 +306,7 @@ 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 @@ -300,6 +317,7 @@ 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 @@ -308,6 +326,7 @@ 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 @@ -317,6 +336,7 @@ 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 @@ -326,6 +346,7 @@ 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 @@ -336,6 +357,7 @@ 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 @@ -344,6 +366,7 @@ 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 @@ -352,6 +375,7 @@ 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. @@ -359,6 +383,7 @@ traits: 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. @@ -366,6 +391,7 @@ traits: 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 @@ -375,6 +401,7 @@ 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 @@ -384,6 +411,7 @@ 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 @@ -393,6 +421,7 @@ 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. @@ -400,6 +429,7 @@ traits: 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 @@ -410,6 +440,7 @@ 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 @@ -419,6 +450,7 @@ 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" diff --git a/data/RBGV_2023/metadata.yml b/data/RBGV_2023/metadata.yml index fc2ed1af3..f3eaf11bb 100644 --- a/data/RBGV_2023/metadata.yml +++ b/data/RBGV_2023/metadata.yml @@ -120,7 +120,6 @@ dataset: taxon_name: taxon_name trait_name: trait_name value: trait_value - value_type: value_type measurement_remarks: measurement_remarks description: Plant morphology data extracted from VicFlora, the Victorian online flora. @@ -163,7 +162,7 @@ contexts: - value: inferred_from_trait description: Trait value inferred from the value of a different trait. - context_property: entity measured - category: entity_context + category: method_context var_in: entity_measured - context_property: replicate observations category: temporal_context @@ -173,6 +172,7 @@ 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 @@ -182,6 +182,7 @@ 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 @@ -190,6 +191,7 @@ 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 @@ -198,6 +200,7 @@ 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 @@ -206,6 +209,7 @@ 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 @@ -214,6 +218,7 @@ 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 @@ -223,6 +228,7 @@ 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 @@ -231,6 +237,7 @@ 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 @@ -239,6 +246,7 @@ 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 @@ -248,6 +256,7 @@ 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 @@ -257,6 +266,7 @@ 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 @@ -265,6 +275,7 @@ 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 @@ -275,6 +286,7 @@ 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 @@ -283,6 +295,7 @@ 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 @@ -292,6 +305,7 @@ 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 @@ -301,6 +315,7 @@ 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 @@ -310,6 +325,7 @@ 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 @@ -319,6 +335,7 @@ 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 @@ -329,6 +346,7 @@ 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 @@ -337,6 +355,7 @@ 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 @@ -346,6 +365,7 @@ 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 @@ -355,6 +375,7 @@ 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 @@ -365,6 +386,7 @@ 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 @@ -373,6 +395,7 @@ 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 @@ -381,6 +404,7 @@ 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. @@ -388,6 +412,7 @@ traits: 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. @@ -395,6 +420,7 @@ traits: 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 @@ -404,6 +430,7 @@ 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 @@ -413,6 +440,7 @@ 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 @@ -422,6 +450,7 @@ 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. @@ -429,6 +458,7 @@ traits: 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 @@ -439,6 +469,7 @@ 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 @@ -448,6 +479,7 @@ 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" diff --git a/data/SAH_2023/metadata.yml b/data/SAH_2023/metadata.yml index 65e97ca43..9e7fa8b27 100644 --- a/data/SAH_2023/metadata.yml +++ b/data/SAH_2023/metadata.yml @@ -103,7 +103,6 @@ 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 SA electronic flora basis_of_record: literature @@ -146,7 +145,7 @@ 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 @@ -156,6 +155,7 @@ 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 @@ -165,6 +165,7 @@ 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 @@ -173,6 +174,7 @@ 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 @@ -181,6 +183,7 @@ 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 @@ -189,6 +192,7 @@ 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 @@ -197,6 +201,7 @@ 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 @@ -206,6 +211,7 @@ 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 @@ -214,6 +220,7 @@ 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 @@ -222,6 +229,7 @@ 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 @@ -231,6 +239,7 @@ 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 @@ -240,6 +249,7 @@ 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 @@ -248,6 +258,7 @@ 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 @@ -258,6 +269,7 @@ 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 @@ -266,6 +278,7 @@ 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 @@ -275,6 +288,7 @@ 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 @@ -284,6 +298,7 @@ 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 @@ -293,6 +308,7 @@ 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 @@ -302,6 +318,7 @@ 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 @@ -312,6 +329,7 @@ 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 @@ -320,6 +338,7 @@ 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 @@ -329,6 +348,7 @@ 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 @@ -338,6 +358,7 @@ 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 @@ -348,6 +369,7 @@ 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 @@ -356,6 +378,7 @@ 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 @@ -364,6 +387,7 @@ 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. @@ -371,6 +395,7 @@ traits: 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. @@ -378,6 +403,7 @@ traits: 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 @@ -387,6 +413,7 @@ 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 @@ -396,6 +423,7 @@ 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 @@ -405,6 +433,7 @@ 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. @@ -412,6 +441,7 @@ traits: 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 @@ -422,6 +452,7 @@ 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 @@ -431,6 +462,7 @@ 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" diff --git a/data/Tsakalos_2020/metadata.yml b/data/Tsakalos_2020/metadata.yml index 6367f0955..82d8ffe23 100644 --- a/data/Tsakalos_2020/metadata.yml +++ b/data/Tsakalos_2020/metadata.yml @@ -85,7 +85,7 @@ locations: description: sclerophyllous scrub and woodland communities contexts: - context_property: leaf surface - category: entity_context + category: method_context var_in: method_context values: - value: abaxial leaf surface diff --git a/data/WAH_2023_1/metadata.yml b/data/WAH_2023_1/metadata.yml index f84d48310..67608ff33 100644 --- a/data/WAH_2023_1/metadata.yml +++ b/data/WAH_2023_1/metadata.yml @@ -128,7 +128,6 @@ 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 long profiles on Florabase, the Western Australia online flora. @@ -165,13 +164,14 @@ 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 traits: - var_in: fruit_colour 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 @@ -181,6 +181,7 @@ 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 @@ -189,6 +190,7 @@ 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 @@ -197,6 +199,7 @@ 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 @@ -205,6 +208,7 @@ 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 @@ -213,6 +217,7 @@ 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 @@ -222,6 +227,7 @@ 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 @@ -230,6 +236,7 @@ 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 @@ -238,6 +245,7 @@ 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 @@ -247,6 +255,7 @@ 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 @@ -256,6 +265,7 @@ 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 @@ -264,6 +274,7 @@ 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 @@ -274,6 +285,7 @@ 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 @@ -282,6 +294,7 @@ 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 @@ -291,6 +304,7 @@ 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 @@ -300,6 +314,7 @@ 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 @@ -309,6 +324,7 @@ 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 @@ -318,6 +334,7 @@ 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 @@ -328,6 +345,7 @@ 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 @@ -336,6 +354,7 @@ 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 @@ -345,6 +364,7 @@ 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 @@ -354,6 +374,7 @@ 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 @@ -364,6 +385,7 @@ 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 @@ -372,6 +394,7 @@ 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 @@ -380,6 +403,7 @@ 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. @@ -387,6 +411,7 @@ traits: 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. @@ -394,6 +419,7 @@ traits: 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 @@ -403,6 +429,7 @@ 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 @@ -412,6 +439,7 @@ 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 @@ -421,6 +449,7 @@ 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. @@ -428,6 +457,7 @@ traits: 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 @@ -438,6 +468,7 @@ 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 @@ -447,6 +478,7 @@ 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" diff --git a/data/WAH_2023_2/metadata.yml b/data/WAH_2023_2/metadata.yml index 707eed9fb..f385fb952 100644 --- a/data/WAH_2023_2/metadata.yml +++ b/data/WAH_2023_2/metadata.yml @@ -129,7 +129,6 @@ 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 short profiles on Florabase, the Western Australia online flora. @@ -170,13 +169,14 @@ 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 traits: - var_in: fruit_colour 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 @@ -186,6 +186,7 @@ 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 @@ -194,6 +195,7 @@ 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 @@ -202,6 +204,7 @@ 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 @@ -210,6 +213,7 @@ 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 @@ -218,6 +222,7 @@ 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 @@ -227,6 +232,7 @@ 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 @@ -235,6 +241,7 @@ 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 @@ -243,6 +250,7 @@ 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 @@ -252,6 +260,7 @@ 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 @@ -261,6 +270,7 @@ 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 @@ -269,6 +279,7 @@ 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 @@ -279,6 +290,7 @@ 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 @@ -287,6 +299,7 @@ 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 @@ -296,6 +309,7 @@ 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 @@ -305,6 +319,7 @@ 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 @@ -314,6 +329,7 @@ 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 @@ -323,6 +339,7 @@ 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 @@ -333,6 +350,7 @@ 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 @@ -341,6 +359,7 @@ 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 @@ -350,6 +369,7 @@ 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 @@ -359,6 +379,7 @@ 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 @@ -369,6 +390,7 @@ 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 @@ -377,6 +399,7 @@ 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 @@ -385,6 +408,7 @@ 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. @@ -392,6 +416,7 @@ traits: 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. @@ -399,6 +424,7 @@ traits: 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 @@ -408,6 +434,7 @@ 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 @@ -417,6 +444,7 @@ 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 @@ -426,6 +454,7 @@ 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. @@ -433,6 +462,7 @@ traits: 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 @@ -443,6 +473,7 @@ 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 @@ -452,6 +483,7 @@ 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"