diff --git a/data/APD_traits_input.csv b/data/APD_traits_input.csv index 54a58d6..3f269ad 100644 --- a/data/APD_traits_input.csv +++ b/data/APD_traits_input.csv @@ -268,9 +268,9 @@ trait_0012121,root_dry_matter_content,Root dry matter content (RDMC),A root mass trait_0012122,root_mass_fraction,Root mass fraction,A root mass trait [TO:0000279] which is the ratio [PATO:0001470] of the total root dry mass [TO:0000078] to whole plant [PO:0000003] dry mass [APD:glossary/40080].,The ratio of total root system dry mass to whole plant dry mass.,,https://w3id.org/APD,STATO_0000251,0.01,1,mg/mg,milligram per milligram,trait_group_0012104,14/07/2021,05/02/2024,,,,PO_0009005; PO_0000003,PATO_0000125; ECSO_00000619; PATO_0001470,,,EnvThes:21360; glossary_40081; PO_0025025,,,,,,,Plant biomass and allometry: Root mass fraction (fraction of root dry mass per whole plant dry mass) [TRY:470] (https://www.try-db.org/de/de.php),,,,,,,,,,,root dry mass [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,, trait_0012221,accessory_cost_fraction,Seed accessory cost fraction,"A reproductive shoot system [PO:0025082] biomass allocation [EnvThes:21360] trait which is one minus the ratio [PATO:0001470] of total plant seed [PO:0009010] dry [PATO:0001824] mass [PATO:0000125] to total plant reproductive shoot system tissue dry mass where reproductive tissues include all flower buds [PO:0000056], flowers [PO:0009046], fruits [PO:0009001], dispersal [EnvThes:21038] tissues, and seeds produced during the developmental process involved in reproduction [GO:0003006].","The fraction of total reproductive investment required to mature a seed that is invested in non-seed tissues. It is calculated as one minus, the ratio of total biomass investment in seeds to total biomass investment in all reproductive tissues, including flower buds, flowers, fruits, dispersal tissues, aborted seeds, and successfully matured seeds.",,https://w3id.org/APD,STATO_0000251,0.01,1,mg/mg,milligram per milligram,trait_group_0012202,14/07/2021,05/02/2024,,,,PO_0025082; PO_0009046; PO_0009001; PO_0009010,PATO_0000125,,Lord & Westoby 2006,EnvThes:21360; GO_0000003; glossary_40004,,,,,,,,Plant biomass and allometry: Reproductive dry mass per plant dry mass (reproductive weight fraction) [TRY:1046] (https://www.try-db.org/de/de.php),,,,,,,,,,,,,,, trait_0012222,accessory_cost_mass,Seed accessory cost mass,"A reproductive shoot system [PO:0025082] biomass allocation [EnvThes:21360] trait which is the sum of the dry [PATO:0001824] mass [PATO:0000125] of all flower buds [PO:0000055], flowers [PO:0009046], fruits [PO:0009001], aborted seeds, and dispersal [EnvThes:21038] tissues produced during the developmental process involved in reproduction [GO:0003006], but excludes mature [PATO:0001701] seed [PO:0009010] dry mass.","The mass of seed accessory costs, which is the total biomass investment in all reproductive tissues, excluding biomass invested in successfully matured seeds; it includes all biomass invested in flower buds, flowers, fruits, dispersal tissues and aborted seeds.",,https://w3id.org/APD,STATO_0000251,0.01,10000,mg,milligram,trait_group_0012202,14/07/2021,05/02/2024,,,,PO_0025082; PO_0009046; PO_0009001; PO_0009010,PATO_0000125,,Lord & Westoby 2006,EnvThes:21360; GO_0000003; glossary_40004,,,,,,,,,,,,,,,,,,,,,,, -trait_0012301,bud_length,Bud length,A floral organ morphology trait [TO:0000862] which is the length [PATO:0000122] of the bud [PO:0000055] from the base of the receptable [PO:0009064] or the base of an inferior ovary [PO:0009072] to the tip of the bud.,"Linear dimension from the base to the apex of a bud, even if this is not the longest dimension.",,https://w3id.org/APD,STATO_0000251,0.01,200,cm,centimetre,trait_group_0012404,05/02/2024,05/02/2024,,,,PO_0025082; PO_0000055,PATO_0000122; PATO_0000117,,,,GO_0000003; PO_0009059; PO_0009058,,,,,,,,,,,,,,,,,,,,,, -trait_0012302,bud_width,Bud width,A floral organ morphology trait [TO:0000862] which is the width [PATO:0000921] of the bud [PO:0000055] from the base of the receptable [PO:0009064] or the base of an inferior ovary [PO:0009072] to the tip of the bud. Width is the greatest linear dimension [PATO:0001708] perpendicular to [PATO:0002434] to the bud length [PATO:0000122],"Greatest linear width dimension of a bud, sometimes referred to as 'diameter' in buds where the width and height are identical; orthogonal to the bud length, the base-to-apex dimension.",,https://w3id.org/APD,STATO_0000251,0.01,200,cm,centimetre,trait_group_0012404,05/02/2024,05/02/2024,,,,PO_0025082; PO_0000055,PATO_0000921; PATO_0000117,,,,GO_0000003; PO_0009059; PO_0009058,,,,,,,,,,,,,,,,,,,,,, -trait_0012351,buds_per_inflorescence,Buds per inflorescence,"A floral organ morphology trait [TO:0000862] which is the count [NCIT:C25463] of buds [PO:0000055] in an inflorescence [PO:0009049], where an inflorescence can be either a single cluster of flowers or the entire reproductive shoot system [PO:0025082].","The count of buds in an inflorescence, where an inflorescence can be either a single cluster of flowers or the entire reproductive shoot system.",,https://w3id.org/APD,STATO_0000251,1,1000,{count}/{count},{count}/{count},trait_group_0012404,05/02/2024,05/02/2024,,,,PO_0025082; PO_0000055; PO_0009049,PATO_0001555; STATO_0000300; PATO_0001470; NCIT_C25463; NCIT_C43414; NCIT_C25201,,,,GO_0000003; PO_0025082; PO_0009049,,,,,,,,,,,,,,,,,,,,,, +trait_0012301,bud_length,Bud length,A floral organ morphology trait [TO:0000862] which is the length [PATO:0000122] of the bud [PO:0000055] from the base of the receptable [PO:0009064] or the base of an inferior ovary [PO:0009072] to the tip of the bud.,"Linear dimension from the base to the apex of a bud, even if this is not the longest dimension.",,https://w3id.org/APD,STATO_0000251,0.01,200,cm,centimetre,trait_group_0012404,5/2/2024,05/02/2024,,,,PO_0025082; PO_0000055,PATO_0000122; PATO_0000117,,,,GO_0000003; PO_0009059; PO_0009058,,,,,,,,,,,,,,,,,,,,,, +trait_0012302,bud_width,Bud width,A floral organ morphology trait [TO:0000862] which is the width [PATO:0000921] of the bud [PO:0000055] from the base of the receptable [PO:0009064] or the base of an inferior ovary [PO:0009072] to the tip of the bud. Width is the greatest linear dimension [PATO:0001708] perpendicular to [PATO:0002434] to the bud length [PATO:0000122],"Greatest linear width dimension of a bud, sometimes referred to as 'diameter' in buds where the width and height are identical; orthogonal to the bud length, the base-to-apex dimension.",,https://w3id.org/APD,STATO_0000251,0.01,200,cm,centimetre,trait_group_0012404,5/2/2024,05/02/2024,,,,PO_0025082; PO_0000055,PATO_0000921; PATO_0000117,,,,GO_0000003; PO_0009059; PO_0009058,,,,,,,,,,,,,,,,,,,,,, +trait_0012351,buds_per_inflorescence,Buds per inflorescence,"A floral organ morphology trait [TO:0000862] which is the count [NCIT:C25463] of buds [PO:0000055] in an inflorescence [PO:0009049], where an inflorescence can be either a single cluster of flowers or the entire reproductive shoot system [PO:0025082].","The count of buds in an inflorescence, where an inflorescence can be either a single cluster of flowers or the entire reproductive shoot system.",,https://w3id.org/APD,STATO_0000251,1,1000,{count}/{count},{count}/{count},trait_group_0012404,5/2/2024,05/02/2024,,,,PO_0025082; PO_0000055; PO_0009049,PATO_0001555; STATO_0000300; PATO_0001470; NCIT_C25463; NCIT_C43414; NCIT_C25201,,,,GO_0000003; PO_0025082; PO_0009049,,,,,,,,,,,,,,,,,,,,,, trait_0012410,flower_androecium_structural_merism,Number of androecium parts in each whorl (Androecium structural merism),"An androecium morphology trait [TO:0000994] which is the total count [NCIT:C25463] of stamens [PO:0009029], staminodes [PO:0009077] or stamen bundles (fascicles [NCIT:C79692]) in each floral whorl [PO:0025023].","The number of stamens or stamen bundles (fascicles) in one whorl, considering both fertile stamens and staminodes.","This character is not applicable for spiral or irregular stamen arrangements, nor when there is a single structural stamen (i.e., one stamen, no staminodes; e.g., Chloranthus, Chloranthaceae). Definition derived from Schoenenberger et al. (2020) for their character '332. Androecium structural merism (C1)'",https://w3id.org/APD,STATO_0000251,0,100,{count},{count},trait_group_0012408,14/07/2021,05/02/2024,24/05/2023,,,PO_0025082; PO_0009046,PATO_0001555; NCIT_C25463,Hervé Sauquet,Schönenberger 2020,GO_0000003; PO_0009061; PO_0009029; PO_0009077; NCIT_C79692; glossary_40060; PO_0025023,,,,,,,,,,,,,,,,,,,,,,, trait_0012411,flower_androecium_structural_phyllotaxis,Androecium structural phyllotaxis,"An androecium morphology trait [TO:0000994] which is the spatial pattern or distribution [PATO:0000060] (phyllotaxy [TO:0006014]) of stamen [PO:0009029], staminodes [PO:0009077] or stamen bundles (fascicles [NCIT:C79692]) in each floral whorl [PO:0025023].","Structural phyllotaxy of the androecium, considering both fertile stamens and staminodes. In cases of stamen fascicles, it is the phyllotaxis of fascicles, not individual stamens that are recorded.","This character is not applicable when there is a single structural stamen (i.e., one stamen, no staminodes; e.g., Chloranthus, Chloranthaceae). Definition and trait values derived from Schoenenberger et al. (2020) for their character '330. Androecium structural phyllotaxy (D1)'",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0012408,14/07/2021,05/02/2024,24/05/2023,,,PO_0025082; PO_0009046,PATO_0000060,Hervé Sauquet,Schönenberger 2020,GO_0000003; PO_0009061; TO_0006014; PO_0009029; PO_0009077; NCIT_C79692; PO_0025023,,,,,,,,,,,,,,,,,,,,,,, trait_0012412,flower_androecium_structural_whorls_count,Number of androecium structural whorls,"An androecium morphology trait [TO:0000994] which is the total count [NCIT:C25463] of whorls [PO:0025023] comprising the androecium [PO:0009061], considering both stamen [PO:0009029] and staminodes [PO:0009077]. If stamens are grouped into fascicles [NCIT:C79692], the trait is the count of whorls of fascicles.","The number of whorls, considering both fertile stamens and staminodes. In cases of stamen fascicles, the count of whorls of fascicles is recorded.","This character is not applicable for spiral or irregular stamen arrangements, or when there is a single structural stamen (i.e., one stamen, no staminodes; e.g., Chloranthus, Chloranthaceae). Definition derived from Schoenenberger et al. (2020) for their character '331. Number of androecium structural whorls (C1)'",https://w3id.org/APD,STATO_0000251,0,100,{count},{count},trait_group_0012408,14/07/2021,05/02/2024,24/05/2023,,,PO_0025082; PO_0009046,PATO_0001555; NCIT_C25463,Hervé Sauquet,Schönenberger 2020,GO_0000003; PO_0009061; PO_0009029; PO_0009077; NCIT_C79692; glossary_40060; PO_0025023,,,,,,,,,,,,,,,,,,,,,,, @@ -451,7 +451,7 @@ trait_0030016,plant_photosynthetic_organ,Plant photosynthetic organ,"A plant str trait_0030017,plant_alternative_energy_and_nutrient_acquisition_strategy,Plant alternative energy and nutrient acquisition strategies,A whole plant [PO:0000003] life history [ECOCORE:00000018] trait which are alternative mechanisms [NCIT:C25343] plants use to obtain [NCIT:C52349] or produce [SIO:001106] energy [PATO:0001021] (carbohydrates [CHEBI:16646]) or nutrients [CHEBI:33284].,"Trait indicating the strategies used by a plant to obtain or produce energy (carbohydrates) or nutrients, including photosynthesis and various saprophytic and carnivorous energy and nutrient acquisition mechanisms.","Although the majority of vascular plants use photosynthesis to produce their own carbohydrates, this trait mostly includes data for the few taxa that are not photosynthetic. Likewise, it captures alternative nutrient acquisition strategies. See also the trait `parasitic` which captures data on whether plants are parasitic (or partially parasitic), forming haustoria to penetrate their host plant. The trait `root_structures` includes specialised root structures",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006,31/10/2022,05/02/2024,,,,PO_0000003; PO_0025034,PATO_0001995; NCIT_C25343,,,PATO_0001021; CHEBI_16646; CHEBI_33284; GO_0040007,,,,,,,,,,,,,,,,,,,,Nutritional relationships [BROT:18] (http://doi.org/10.1038/sdata.2018.135),,, trait_0030018,woodiness,Woodiness,"A whole plant [PO:0000003] phenotype [NCIT:C16977] trait which indicates whether the plant stem [PO:0009047] (the vegetative shoot system [PO:0025607]) is woody, with “woody” defined to include both plant stems with secondary xylem (true wood) [PO:0005848] and those with wood-like lignification [CHEBI:6457] (woodiness in monocots and ferns).","A binary trait, indicating whether a plant's stems are woody, with woody broadly defined to include both `true wood` (secondary xylem) and taxa that do not produce secondary xylem (i.e. monocots and ferns) but have thick, stiff, robust lignified stems.",This trait considers all species that have stiff lignified stems as `woody` and those that lack such stems as `herbaceous`. See the trait `plant woodiness detailed` for sub-categories of `woody` that indicate the extent and type of woodiness present in a plant stem.,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006; trait_group_0011802,14/07/2021,05/02/2024,31/10/2022,,Vascular plants,PO_0000003; PO_0009047,PATO_0000025; PATO_0000141,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; LEDA Data Standards 2005,PO_0005848; CHEBI_6457; FLOPO_0900038; NCIT_C93062; PATO_0002352,,FLOPO_0900038; EnvThes:20744,,,Woodiness [TOP706] (https://top-thesaurus.org/index),,,Plant woodiness [TRY:38] (https://www.try-db.org/de/de.php),,,woodiness and stem specific density [LEDA:3.1] (https://uol.de/en/landeco/research/leda/standards),,,,,whole plant woodiness [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, trait_0030019,woodiness_detailed,Detailed woodiness categories,"A whole plant [PO:0000003] phenotype [NCIT:C16977] trait which indicates the vertical [PATO:0001854] extent, distribution [PATO:0000060], and type [NCIT:C25284] of wood present in stems [PO:0009047], roots [PO:0009005], and reproductive shoot systems [PO:0025082], distinguishing between plants with secondary xylem (true wood) [PO:0005848] versus wood-like lignification [CHEBI:6457] (woodiness in monocots and ferns).","Trait indicating the extent, distribution, and type of secondary xylem (true wood) and wood-like lignification (woodiness in monocots and ferns) in stems, roots, and reproductive shoots.","This trait documents in detail the degree and type of lignification in a plant's stems and roots (woodiness), while `plant woodiness` is a binary trait collapsing woodiness into a pair of values, `woody` versus `herbaceous`. Datasets that only use the terms `woody` versus `herbaceous` are only mapped to the binary trait; only datasets that explicitly indicate different levels of woodiness are mapped to `plant woodiness detailed`.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006; trait_group_0011802,31/10/2022,05/02/2024,31/10/2022,,Vascular plants,PO_0000003; PO_0009047; PO_0009005; PO_0025082,PATO_0000025; PATO_0000141; PATO_0000060,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; LEDA Data Standards 2005; Carlquist 2013,PO_0005848; CHEBI_6457; FLOPO_0900038; NCIT_C93062; PATO_0002352,,FLOPO_0900038; EnvThes:20744,,,Woodiness [TOP706] (https://top-thesaurus.org/index),,,Plant woodiness [TRY:38] (https://www.try-db.org/de/de.php),,,woodiness and stem specific density [LEDA:3.1] (https://uol.de/en/landeco/research/leda/standards),,,,,,whole plant woodiness [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,, -trait_0030020,plant_physical_defence_structures,Physical defence structures,"A plant structure morphology trait [TO:0000839] which indicates the plant structures [PO:0009011] used for defence [NCIT:C61556], including spine leaves [PO:0025173], spine stipules [PO:0025174], spine petiole [PO:0025613], thorns [PO:0025172], and prickles [PO:0025169].","The presence (or explicit absence) of specific physical defence structures on a plant, including spines, thorns, prickles, and sharp-tipped leaves.","This trait identifies explicit physical defence structures on a plant. The trait `plant_spinescence` indicates the degree of defence afforded to plants, with values defined by Pérez-Harguindeguy et al. 2013 (doi:10.1071/BT12225).",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0011001; trait_group_0011202; trait_group_0011802; trait_group_0012002,14/07/2021,05/02/2024,31/10/2022,physical_defence,none,PO_0025034; PO_0009047; PO_0004518; PO_0000003,PATO_0000141; PATO_0001925; PATO_0000052,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; Hanley 2007,PO_0025173; PO_0025174; PO_0025172; PO_0025169; NCIT_C61556; PO_0025613,,EnvThes:21109,,,,,,"Shoot emergences (pubescence, hairs, spines, thorns) [TRY:677] (https://www.try-db.org/de/de.php); Shoot emergences (pubescence, hairs, spines, thorns) [TRY:1255] (https://www.try-db.org/de/de.php); Shoot emergences (pubescence, hairs, spines, thorns) [TRY:1256] (https://www.try-db.org/de/de.php)",,,,,,leaf_spines_1 [GIFT:4.13.1] (https://www.try-db.org/de/de.php); leaf_thorns_1 [GIFT:4:14.1] (https://www.try-db.org/de/de.php); defence [GIFT:6.5] (https://gift.uni-goettingen.de),,,,,,,Basic leaf shape [BROT:5] (http://doi.org/10.1038/sdata.2018.135),,Armature [PalmTraits] (https://doi.org/10.1038/s41597-019-0189-0) +trait_0030020,plant_physical_defence_structures,Physical defence structures,"A plant structure morphology trait [TO:0000839] which indicates the plant structures [PO:0009011] used for defence [NCIT:C61556], including spine leaves [PO:0025173], spine stipules [PO:0025174], spine petiole [PO:0025613], thorns [PO:0025172], and prickles [PO:0025169].","The presence (or explicit absence) of specific physical defence structures on a plant, including spines, thorns, prickles, and sharp-tipped leaves.","This trait identifies explicit physical defence structures on a plant. The trait `plant_spinescence` indicates the degree of defence afforded to plants, with values defined by Pérez-Harguindeguy et al. 2013 (doi:10.1071/BT12225).",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0011001; trait_group_0011202; trait_group_0011802; trait_group_0012002,14/07/2021,05/02/2024,31/10/2022,physical_defence,none,PO_0025034; PO_0009047; PO_0004518; PO_0000003,PATO_0000141; PATO_0001925; PATO_0000052,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; Hanley 2007,PO_0025173; PO_0025174; PO_0025172; PO_0025169; NCIT_C61556; PO_0025613,,EnvThes:21109,,,,,,"Shoot emergences (pubescence, hairs, spines, thorns) [TRY:677] (https://www.try-db.org/de/de.php); Shoot emergences (pubescence, hairs, spines, thorns) [TRY:1255] (https://www.try-db.org/de/de.php); Shoot emergences (pubescence, hairs, spines, thorns) [TRY:1256] (https://www.try-db.org/de/de.php)",,,,,,leaf_spines_1 [GIFT:4.13.1] (https://gift.uni-goettingen.de); leaf_thorns_1 [GIFT:4.14.1] (https://gift.uni-goettingen.de); defence [GIFT:6.5] (https://gift.uni-goettingen.de),,,,,,,Basic leaf shape [BROT:5] (http://doi.org/10.1038/sdata.2018.135),,Armature [PalmTraits] (https://doi.org/10.1038/s41597-019-0189-0) trait_0030021,plant_climbing_mechanism,Plant climbing mechanisms,A whole plant [PO:0000003] phenotype [NCIT:C16977] trait that indicates stem [PO:0009047] and leaf [PO:0025034] structures [PATO:0000141] and physical mechanisms [NCIT:C25343] a plant uses to climb [NCIT:C81002] up other plants or substrates.,"Mechanisms plants use to climb, including both specialised leaf and stem adaptations and stem growth habits.",,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006; trait_group_0011202; trait_group_0011802,14/07/2021,05/02/2024,31/10/2022,vine_climbing_mechanism,climbing and scrambling plants,PO_0000003; PO_0009047; PO_0025034,PATO_0000141; NCIT_C25343,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; Gallagher 2012,NCIT_C81002; NCIT_C61460,,,,,,,,,Plant growth form [TRY:42] (https://www.try-db.org/de/de.php),,,,,,,,,,,,,, trait_0030022,plant_succulence,Plant succulence,"A whole plant [PO:0000003] phenotype [NCIT:C16977] trait that indicates whether any plant tissues [CARO:0000043] are succulent [FLOPO:0900041], indicating they are thick [PATO:0000591] and fleshy [PATO:0002351], generally storing water [CHEBI:15377] as a drought tolerance [TO:0000276] adaptation or filling with water as a salt tolerance [TO:0006001] adaptation.","Trait indicating whether the leaves or stems of a plant are thick and fleshy because they store water, generally an adaptation to arid or salty environments.",Succulence generally has either a water storage function or is a mechanism to cope with (or thrive in) saline conditions. See the categorical trait `plant_tolerance_salt` for plant salt tolerance and salt avoidance strategies and the numeric trait `plant_tolerance_soil_salinity` for the soil salinity a plant can tolerate.,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006; trait_group_0030704; trait_group_0011802; trait_group_0011202,31/10/2022,05/02/2024,31/10/2022,,none,PO_0000003; PO_0009047; PO_0025034,PATO_0000141; PATO_0001995,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Pérez-Harguindeguy 2013; Simpson 2019; Ogburn & Edwards 2010,FLOPO_0900041; CHEBI_15377; TO_0000276; TO_0006001; PATO_0085001; PATO_0002351,FLOPO_0900041,,,,,,,,Plant growth form [TRY:42] (https://www.try-db.org/de/de.php),,,,plant_succulence [GIFT:4.16.1] (https://gift.uni-goettingen.de),,,,,,,,Basic leaf shape [BROT:5] (http://doi.org/10.1038/sdata.2018.135),, trait_0030023,stem_growth_habit,Stem growth habit,"A whole plant [PO:0000003] phenotype [NCIT:C16977] trait that indicates the structure [PATO:0000141] and 3-dimensional extent [PATO:0001710] of a plant's vegetative shoot system [PO:0025607], including the position [PATO:0000140] of stems [PO:0009047], degree of branchiness [PATO:0002009], density [PATO:0001019] of branches [PO:0025073], and branch angles [PATO:0002326] relative to each other and the ground surface [sweetontology.net/realmSoil/Ground].","Trait characterising a stem's structure and 3-dimensional extent, including the position of stems, degree of branchiness, density of branches, and branch angles relative to other branches and the ground surface.","This trait captures how a plant explores 3-dimensional space, with trait values predominantly adjectives that modify the core plant growth forms.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030006; trait_group_0011802,14/07/2021,05/02/2024,31/10/2022,growth_habit,none,PO_0000003; PO_0009047; PO_0025034,PATO_0000052; PATO_0001710; PATO_0000140; PATO_0002326; PATO_0000141; PATO_0000060,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019,PO_0025607; PATO_0002009; GO_0040007,,,,,,,,,,,,Shoot growth form [LEDA:3.2] (https://uol.de/en/landeco/research/leda/standards); Leaf distribution along the stem [LEDA:3.3] (https://uol.de/en/landeco/research/leda/standards),shoot_orientation [GIFT:1.9.1] (https://gift.uni-goettingen.de),,climber_2 [GIFT:1.4.2] (https://gift.uni-goettingen.de),,,,,,,, @@ -461,7 +461,7 @@ trait_0030026,competitive_stratum,Competitive stratum,"A classification [NCIT:C2 trait_0030027,nitrogen_fixing,Plant nitrogen fixation capacity,"A trait which indicates whether a plant has the capacity to engage in symbioses [GO:0044403] with microorganisms [NCIT:C14329] (bacteria [NCIT:C14187], cyanobacteria [NCBITaxon:1117], and fungi [NCBITaxon:4751]) capable of nitrogen fixation [GO:0009399] and usually identified by nodulation [GO:0009877] on the plant roots [PO:0009005].","Binary variable describing whether a plant has the capacity for nitrogen fixatation, indicating it engages in symbioses with microorganisms (most commonly bacteria or cyanobacteria) that are capable of nitrogen fixation. Nitrogen fixation capacity is usually identified by nodules on the plant roots.",,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030009; trait_group_0012104,14/07/2021,05/02/2024,,,,PO_0000003; PO_0009005,PATO_0001995,,,GO_0044403; GO_0009399; GO_0009877; NCIT_C14329; GO_0085030; ECOCORE_00000022,EnvThes:22051,,TO_0000900,,,,Plant nitrogen(N) fixation capacity [TRY:8] (https://www.try-db.org/de/de.php),,,,,,nitrogen_fix_1 [GIFT:4.5.1] (https://gift.uni-goettingen.de),,,,,,,Nutritional relationships [BROT:18] (http://doi.org/10.1038/sdata.2018.135),,, trait_0030028,root_structure,Plant root structures,"A trait which indicates types [NCIT:C25284] of root [PO:0009005] structures [PATO:0000141], including structures associated with mutualisms [GO:0085030] with mycorrhizae [EnvThes:20656].","Specific specialized types of root structures and root symbioses, especially symbioses with mycorrhizal fungi.",,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030009; trait_group_0012104,14/07/2021,05/02/2024,,,,PO_0000003; PO_0009005,PATO_0001995; PATO_0000141,,Brundrett 2008,GO_0085030; EnvThes:20656; GO_0036377; GO_0044403; GO_0085035; NCIT_C14329; ECOCORE_00000022,,,,,,,Mycorrhiza type [TRY:7] (https://www.try-db.org/de/de.php),,,,,,mycorrhiza_1 [GIFT:6.4.1] (https://gift.uni-goettingen.de),,,,,,,Nutritional relationships [BROT:18] (http://doi.org/10.1038/sdata.2018.135),,, trait_0030029,parasitic,Plant parasitism status,"A whole plant [PO:0000003] phenotype [NCIT:C16977] trait that indicates if a plant is involved in a parasitic [ECOCORE:00000146] symbiosis [ECOCORE:00000022] where it forms haustorium [GO:0085035] on a host [GO:0018995] plant and the host plant provides all or some of its high energy [PATO:0001021] carbon [CHEBI:27594] compounds [NCIT:C43366], mineral nutrition (nutrients [CHEBI:33284]) and/or water [CHEBI:15377].","Trait indicating whether a plant forms haustoria and obtains part or all of its energy-rich carbon compounds (photosynthetic sugars), mineral nutrition and/or water directly from another plant (its host) in an interaction that does not benefit the host plant.","Plants described as parasitic in the context of this trait always have haustoria, specialised organs that penetrate the host plants's vascular bundles. The trait `root_structures` documents symbiotic relationships with fungi. The trait `plant_energy_acquisition_strategy` documents specialised strategies or specialised organs or tissues plants use to obtain carbon or mineral nutrition.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030009,14/07/2021,05/02/2024,31/10/2022,,none,PO_0000003,PATO_0001995; PATO_0000141,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Ian J. Wright; Peter Vesk; Gregory J. Jordan; Andy Leigh; Patricia Lu-Irving; Lily Dun; David Coleman,Simpson 2019; T?šitel 2016; Nickrent & Musselman 2004,ECOCORE_00000146; ECOCORE_00000022; GO_0085035; PATO_0001021; CHEBI_33284; GO_0072519; GO_0044403,,,,,,,,,,,,,,parasite_1 [GIFT:1.5.1] (https://gift.uni-goettingen.de),,,,,,Nutritional relationships [BROT:18] (http://doi.org/10.1038/sdata.2018.135),,, -trait_0030060,sex_type,Plant sex type,"A plant structure morphology trait [TO:0000839] which is the distribution [PATO:0000060] of male [PATO:0000384], female [PATO:0000383], and hermaphroditic [PATO:0001340] flowers [PO:0009046] on one individual [EFO:0000542] and across multiple individuals in a population [PCO:0000001].","Plant sex type, indicating, for a taxon the type of flowers (male, female, and hermaphroditic) present on individual plants versus separate plants within a population.",,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0011001,14/07/2021,05/02/2024,,,,PO_0000003; PO_0009046,PATO_0001995; PATO_0000060,,,PATO_0001340; PATO_0001894,,EnvThes:21061,,Plant dicliny type [TOP295] (https://top-thesaurus.org/index),,,"Flower sexual syndrome (dichogamy, cleistogamy, dioecious, monoecious) [TRY:915] (https://www.try-db.org/de/de.php)",,,,,,,reproduction_sexual_1 [GIFT:1.4.1] (https://gift.uni-goettingen.de),,whole plant sexual system [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, +trait_0030060,sex_type,Plant sex type,"A plant structure morphology trait [TO:0000839] which is the distribution [PATO:0000060] of male [PATO:0000384], female [PATO:0000383], and hermaphroditic [PATO:0001340] flowers [PO:0009046] on one individual [EFO:0000542] and across multiple individuals in a population [PCO:0000001].","Plant sex type, indicating, for a taxon the type of flowers (male, female, and hermaphroditic) present on individual plants versus separate plants within a population.",,https://w3id.org/APD,STATO_0000252,,,,,trait_group_0011001,14/07/2021,05/02/2024,,,,PO_0000003; PO_0009046,PATO_0001995; PATO_0000060,,,PATO_0001340; PATO_0001894,,EnvThes:21061,,Plant dicliny type [TOP295] (https://top-thesaurus.org/index),,,"Flower sexual syndrome (dichogamy, cleistogamy, dioecious, monoecious) [TRY:915] (https://www.try-db.org/de/de.php)",,,,,,,reproduction_sexual_1 [GIFT:3.4.1] (https://gift.uni-goettingen.de),,whole plant sexual system [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, trait_0030061,pollination_syndrome,Pollination syndrome,A classification [NCIT:C25161] based on a taxon's [NCIT:C40098] flower morphology traits [TO:0000499] that indicates the taxa (biotic vectors) or abiotic mechanisms [NCIT:C25343] that most likely pollinate [GO:0009856] a flower [PO:0009046].,"For a given taxon, the biotic vectors (including explicit taxa) or abiotic mechanisms that are most likely to pollinate its flowers, based on the taxon's flower morphology.","Trait values include both very specific terms and quite general ones, reflecting the variation in detail provided across studies.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0012404; trait_group_0030009,14/07/2021,05/02/2024,23/02/2023,,applicable to seed plants (gymnosperms and angiosperms),PO_0025082; PO_0009046,PATO_0001995; NCIT_C25343,Ruby Stephens,Ollerton 2019; Dellinger 2020,GO_0009856; GO_0085030; GO_0044403; glossary_40086; GO_0000003; ECOCORE_00000022,,,,Flower pollination syndrome [TOP333] (https://top-thesaurus.org/index),,,pollination syndrome [TRY:29] (https://www.try-db.org/de/de.php),,,,,,pollination_syndrom [GIFT:3.6] (https://gift.uni-goettingen.de),,,flower pollination syndrome [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, trait_0030062,pollination_system,Pollination system,A classification [NCIT:C25161] based on explicit field studies of pollination [GO:0009856] in the taxon's [NCIT:C40098] native range (preferred) or else a combination of a taxon's flower morphology traits [TO:0000499] (that suggest specific [NCIT:C38024] taxa (biotic vectors) or abiotic mechanisms [NCIT:C25343] that most likely pollinate [GO:0009856] a flower [PO:0009046]) and the pollinators actually observed visiting the taxon's flower.,"For a given taxon, the biotic vectors (including explicit taxa) or abiotic mechanisms that are most likely to pollinate its flowers, based on explicit field studies of pollination in the taxon's native range (preferred) or else a combination of possible pollinators observed visiting a taxon's flowers and the taxon's flower morphology.","Trait values include both very specific terms and quite general ones, reflecting the variation in detail provided across studies.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0012404; trait_group_0030009,14/07/2021,05/02/2024,23/02/2023,,applicable to seed plants (gymnosperms and angiosperms),PO_0025082; PO_0009046,PATO_0001995; NCIT_C25343,Ruby Stephens,Ollerton 2019,GO_0009856; GO_0085030; GO_0044403; glossary_40086; GO_0000003; ECOCORE_00000022,,,,,,,,pollination syndrome [TRY:29] (https://www.try-db.org/de/de.php),,,,,,self_fertilization_1 [GIFT:3.1.1] (https://gift.uni-goettingen.de),,,,,,,,, trait_0030080,genome_size,Plant genome size,The total mass [PATO:0000125] of chromosomes [NCIT:C13202] that comprise a plant's genome [OMIT:0027643] in a somatic cell [CL:0002371].,"Mass of all chromosomes, the genome, in a somatic cell.",,https://w3id.org/APD,STATO_0000251,0.5,100,pg,picogram,trait_group_0030059,14/07/2021,05/02/2024,,,,PO_0000003,PATO_0000125,,,OMIT_0027643; CL_0002371; NCIT_C13202,OMIT_0027643,,,,,,Species genotype: genome size [TRY:1022] (https://www.try-db.org/de/de.php),,,,,,,,,,,,,,,, @@ -471,7 +471,7 @@ trait_0030211,dispersal_syndrome,Diaspore dispersal syndrome,A classification [N trait_0030212,dispersers,Diaspore dispersal agents,The taxa [NCIT:C40098] (biotic vectors) and abiotic mechanisms [NCIT:C25343] that disperse [OMIT: 0027297] seeds [PO:0009010] and fruit [PO:0009001] away from a parent plant.,"Dominant diaspore dispersal agents, including both biotic agents (specific taxa) or abiotic mechanisms responsible for dispersing seeds (or other dispersal units) away from the parent plant.","Allowable terms for biotic dispersal agents include taxa at both the species-level and much broader groupings, reflecting both the different levels of resolution provided by researchers and whether a plant has specific versus broad dispersal agents. Abiotic dispersal mechanisms can likewise be quite general or specific, depending on data availability.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030009,14/07/2021,05/02/2024,30/11/2021,,,PO_0025082; PO_0009010; PO_0009001,PATO_0001995; NCIT_C25343,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Carl Gosper; Lydia Guja; Gregory J. Jordan; Mark Ooi; Karen D. Sommerville; Lily Dun,Pérez-Harguindeguy 2013; Saatkamp 2018; Wigley 2020; LEDA Data Standards 2005; Kew Seed Information Database 2022,GO_0085030; GO_0044403; EnvThes:21042; ECOCORE_00000022,,,,,Plant dispersal syndrome [TOP346] (https://top-thesaurus.org/index),,,Dispersal syndrome [TRY:28] (https://www.try-db.org/de/de.php),,,,,,,,,,,,,,, trait_0030213,flowering_cues,Environmental flowering cues,"Unpredictable, irregular environmental conditions [ENVO_01000203] that are linked to a plant [PO:0000003] producing flowers [PO:0009046].","A plants' flowering response to unpredictable, irregular environmental cues.","Taxa may be scored as having an environmental flowering cue, but also display a season-specific flowering response which is captured in the trait `flowering_time`. For additional details on a plant's post-fire flowering response see also the trait `post_fire_flowering`.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008; trait_group_0030704,19/05/2023,05/02/2024,,,,PO_0025082; PO_0009046,PATO_0000165; PATO_0001309,,,PO_0007016; TO_0002616; ENVO_01000203; EnvThes:20373,,,,,,,,,,,,,,,,,,,,,,, trait_0030214,flowering_time,"Flowering time, by month",The months [UO:0000035] during which a plant [PO:0000003] has open (anthetic) flowers [PO:0009046] and is therefore at the whole plant flowering stage [PO:0007016].,Months during which taxon has open (anthetic) flowers.,"Trait keyed as a sequences of 12 Ns (not flowering) and Ys (flowering), representing the 12 months, starting with January.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008,14/07/2021,05/02/2024,30/11/2021,,,PO_0025082; PO_0009046,PATO_0000165; PATO_0001309; EnvThes:21586,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Carl Gosper; Lydia Guja; Gregory J. Jordan; Mark Ooi; Karen D. Sommerville; Lily Dun,Saatkamp 2018; Stephens 2022,PO_0007016; TO_0002616,,EnvThes:21649,PO_0007016 ,,,Plant flowering begin trait [TOP292] (https://top-thesaurus.org/index); Plant flowering end trait [TOP293] (https://top-thesaurus.org/index),"Flower onset of flowering (first flowering date, flowering beginning) [TRY:2956] (https://www.try-db.org/de/de.php)",,,,,,flowering_time [GIFT:3.7] (https://gift.uni-goettingen.de),,,plant flowering duration [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),plant flowering begin [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,, -trait_0030215,fruiting_time,"Fruiting time, by month",The months [UO:0000035] during which a plant [PO:0000003] produces fruit [PO:0009001] with mature [PATO:0001701] seeds [PO:0009010].,Months during which taxon produces fruit with mature seeds.,"Trait keyed as a sequences of 12 Ns (not flowering) and Ys (flowering), representing the 12 months, starting with January.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008,14/07/2021,05/02/2024,30/11/2021,,,PO_0025082; PO_0009001,PATO_0000165; PATO_0001309; EnvThes:21586,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Carl Gosper; Lydia Guja; Gregory J. Jordan; Mark Ooi; Karen D. Sommerville; Lily Dun,Saatkamp 2018,PO_0025500,,,,,,,,,,,,,Fuiting time [GIFT:3.8] (https://gift.uni-goettingen.de),,,plant fruiting duration [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, +trait_0030215,fruiting_time,"Fruiting time, by month",The months [UO:0000035] during which a plant [PO:0000003] produces fruit [PO:0009001] with mature [PATO:0001701] seeds [PO:0009010].,Months during which taxon produces fruit with mature seeds.,"Trait keyed as a sequences of 12 Ns (not flowering) and Ys (flowering), representing the 12 months, starting with January.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008,14/07/2021,05/02/2024,30/11/2021,,,PO_0025082; PO_0009001,PATO_0000165; PATO_0001309; EnvThes:21586,Elizabeth Wenk; Hervé Sauquet; Russell Barrett; Carl Gosper; Lydia Guja; Gregory J. Jordan; Mark Ooi; Karen D. Sommerville; Lily Dun,Saatkamp 2018,PO_0025500,,,,,,,,,,,,,Fruiting time [GIFT:3.8] (https://gift.uni-goettingen.de),,,plant fruiting duration [BIEN] (https://bien.nceas.ucsb.edu/bien/biendata),,,,,,, trait_0030216,recruitment_time,"Seedling recruitment time, by month",The months [UO:0000035] during which seed [PO:0009010] germination [GO:0009845] and seedling establishment [EnvThes:20410] occurs.,The months during which seed germination and seedling establishment occurs.,"Trait keyed as a sequences of 12 Ns (not flowering) and Ys (flowering), representing the 12 months, starting with January.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008; trait_group_0030704; trait_group_0030602,19/05/2023,05/02/2024,31/05/2023,,,PO_0000003; PO_0009010,PATO_0000165; PATO_0001995,Elizabeth Wenk; Rachael Gallagher; Russell Barrett; Carl Gosper; Rachael Nolan; Tony Auld; Tom Le Breton; Matthew White; Sophie Yang,Auld 1990,GO_0009845; Recruitment; EnvThes:20698; EnvThes:20410; GO_0000003,,,,,,,,,,,,,,,,,,,,,,, trait_0030217,seedling_establishment_conditions,Seedling establishment conditions,"The environmental conditions [ENVO:01000203] under which a taxon [NCIT:C40098] displays seed [PO:0009010] germination [GO:0009845] and seedling establishment [EnvThes:20410], with trait values reflecting successional changes to the vegetation community.","The environmental conditions under which a taxon's seedlings can establish, with trait values reflecting successional changes to the vegetation community.","The selection of trait values does not distinguish between the ability to establish in intermediate age versus mature vegetation, as this level of detail is rarely provided in datasets.",https://w3id.org/APD,STATO_0000252,,,,,trait_group_0030008; trait_group_0030704; trait_group_0030602,19/05/2023,05/02/2024,31/05/2023,,,PO_0000003; PO_0009010,PATO_0000165; PATO_0001995,Elizabeth Wenk; Rachael Gallagher; Russell Barrett; Carl Gosper; Rachael Nolan; Tony Auld; Tom Le Breton; Matthew White; Sophie Yang,,GO_0009845; Recruitment; EnvThes:20698; EnvThes:20410; GO_0000003; ENVO_01000203,,,,,,,,,,,,,,,,,,,,,,, trait_0030218,reproductive_light_environment_index,Canopy light environment required for reproduction,A plant phenological [TO:0000933] life history [ECOCORE:00000018] trait which is an index [NCIT:C25390] that captures the level of photosynthetically active radiation [ENVO:01001864] required by plants for reproduction [GO:0000003].,"The minimum light environment required by plants for reproduction, scaled from 0 to 8.","0 indicates `No direct light, extremely low levels of transmitted/reflected light, such as beneath dense fern or palm fronds close to ground level.`; 0.5 indicates `No direct light, very low levels of transmitted light`; 1 indicates `Rare or no exposure to direct light from lateral sources, and low levels of transmitted light.`; 2 indicates `Low lateral light and low-moderate transmitted light with <10% of inverted cone exposed to lateral sources of direct light, plus low to moderate levels of transmitted light`; 3 indicates `Low-moderate lateral & moderate transmitted light, with <5% exposure of the focal crown to vertical direct light, and <15 % of inverted cone exposed to lateral sources of direct light, plus moderate transmitted light.`; 4 indicates `Moderate lateral light & moderate-high transmitted light, with 5 - 10% exposure of focal crown to direct vertical light, plus 2-20% exposure of inverted cone to lateral sources of direct light, plus moderate to high levels of transmitted light.`; 5 indicates `Moderate vertical light and moderate-high lateral light, with 5 - 20% exposure of focal crown to direct vertical light, plus one or both of, i. 10-40% exposure of 90-degree inverted cone to lateral sources of direct light, ii. exposure to high levels of transmitted light`; 6 indicates `Moderate-High vertical and high lateral light, with 10-30% of vertical projection of the crown exposed to vertical light, and lateral light exposure for > 40% of 90-degree inverted cone`, 7 indicates `High vertical and lateral light, with 30-80% of vertical projection of the crown exposed to vertical light, or exposure to lateral sources of direct light for > 60 % of a 90-degree inverted cone encompassing the focal crown.`; 8 indicates `Full light exposure of crown, with > 80% of the vertical projection of the crown exposed to vertical light.`.",https://w3id.org/APD,STATO_0000251,0,8,{dimensionless},{dimensionless},trait_group_0030008,14/07/2021,05/02/2024,,,,PO_0000003,PATO_0000077; NCIT_C43414; NCIT_C25201,,Wells 2012,ENVO_01001864; GO_0000003; ENVO_01000203; Recruitment; ENVO_01001023,,,EnvThes:21436,,,,,,,,,,,,,,,,,,,,