rebipp/ppi

REBIPP: Plant-Pollinator Interactions Data Vocabulary

ppi's Issues

fruitMass

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	fruiMass
Definition	The mass in grams of a fruit of a flower exposed to a single visitor.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

heterospecificPollenGrainsQuantity

Term definition:

The number of heterospecific pollen grains deposited on the stigma(s) of a flower exposed to multiple visitors

@pzermoglio:

some definitions apply to single visitors, some others to multiple visitors, and I'm not sure I understand why in all cases.

standingCropNectarVolume

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	standingCropNectarVolume
Definition	The total volume in microliters of nectar available to visitors at a given time of a flower longevity.
Comments
Examples	5, 10, 8.5
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

floralSymmetry

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	floralSymmetry
Definition	The symmetry describing whether, and how, a flower, in particular its perianth, can be divided into two or more identical or mirror-image parts.
Comments	There are essentially two main types of symmetry in flowers: bilateral symmetry (also termed zygomorphic, dorsiventral, lateral or irregular) and radial symmetry (also termed actinomorphic or regular). Recommended best practice is to use a controlled vocabulary such as Phenotype and Ant Trait Ontology (PATO)
Examples	zygomorphic, http://purl.obolibrary.org/obo/PATO_0001327
Controlled vocabulary	Phenotype And Trait Ontology
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

Add term - nectarVolumeInMicroliters

The term accumlatedNectarVolume is related to the nectar volume accumulated at the end of a flower longevity which was prevented from visiting.

accumulated: not sufficient to capture non-accumulated measures of nectar volume; ex: two or more measurements of nectar volume were taken during the flower longevity.

The new term nectarVolumeInMicroliters will make possible to share, in conjunction with nectarConcentration, multiple measurements of nectar dynamics, instead of just the volume/concentration of the accumulated nectar.

Term definition (proposal):
The nectar volume in microliters at a specific period of the flower's longevity

This definition makes no assumption or statement about to a specific period of a flower longevity (opposed to: at the end of a flower longevity). So, how can we specify that period using a discrete or continuous data-time representation?

Options:

• Use obis:ExtendedMeasurementOrFact (eMOF) class . The terms of eMOF class can be used in conjunction with an external vocabulary for plant-pollinator interactions. The term dwc:measurementDeterminedDate should be used to define the period of a flower longevity in which the measurement was made. Additionally, the vocabulary should includes terms like nectar volume and microliters to be used with obis:measurementTypeID and obis:measurementUnitID.

• Add a new term to share the specific date-time when a nectar volume measurement was made.

standingCropFlowerLongevity

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	standingCropFlowerLongevity
Definition	The elapsed time in hours or an enumerated value between the moment in which a flower opens and its senescence, describing when the standing crop measures were taken during the flower longevity.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

accumlatedNectarVolume and accumulatedNectarConcentration definition

The actual definition of accumulatedNectarConcentration is:
The total volume in microliters of nectar accumulated at the end of a flower lifespan which was prevented from visiting

The definition makes explicit when and how the nectar volume should be measured. Should we change it to make it more general? Maybe create a new term for nectar volume measurements (not the accumulated volume): nectarVolume.

Can the accumulated nectar be calculated from a set of nectarVolume measurements of a particular flower, a particular plant or for the whole dataset?

availableFlowerQuantity

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	availableFlowerQuantity
Definition	The number or enumeration value for the quantity of open flowers or inflorescences available to visitors.
Comments
Examples	0, 30, 40
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

ovuleQuantity

Term definition:

A number of ovules in flower(s) of the represented plant species.

The number of ovules are actually measured or is it a species trait from literature?

standingCropNectarConcentration

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	standingCropNectarConcentration
Definition	The concentration of nectar, as a percentage of sugar, available to visitors at a given time of a flower longevity.
Comments
Examples	25,75
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

collectingBodyPart

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	collectingBodyPart
Definition	The animal body part (e.g. organ) used to access the floral resources.
Comments
Examples	glossa, bill, tongue, http://purl.obolibrary.org/obo/HAO_0000376
Controlled vocabulary	Hymenoptera Anatomy Ontology Portal
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

flowerShape

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	florwerShape
Definition	The overall shape of the flowers.
Comments	Recommended best practice is to use a controlled vocabulary.
Examples	bush, campanulate, tube
Controlled vocabulary	brush; campanulate; bell-shaped; lantern; trumpet-shaped; open disk (bowl); spherical; tube; keel; iris-type flower, orchid flowers; composite; trap
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

styleLength

Term definition:

The average length, from the base to the tip, of the style(s) of the flower(s) of the plant for which the ‘Interaction’ was recordedof this plant Occurrence

@pzermoglio:

of all styles of all flowers of the plant?

standingCropFlowerLongevityProperty

Term definition:
The elapsed time in hours or an enumerated value between the moment in which a flower opens and its senescence, describing when the standing crop measures were taken during the flower longevity

@pzermoglio:

this is confusing with the first part of the definition. Is it the lifespan of the flower (eg "The elapsed time in hours between the moment in which a flower opens and its senescence") or is it when it was measured? There are two completely different concepts here, longevity and time of measurement

flowerType

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	flowerType
Definition	The type of flower describing whether the flower's corolla opens or not, exposing its reproductive parts to floral visitors (cleistogamous, chasmogamous or mixed).
Comments	Recommended best practice is to use a controlled vocabulary. Example: Plant Trait Ontology
Examples	cleistogamous, chasmogamous, http://purl.obolibrary.org/obo/TO_0000882
Controlled vocabulary	Plant Trait Ontology
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

seedMass

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	seedMass
Definition	The mass in miligrams of mature seeds of a fruit from a flower exposed to a single visitor.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

apomiticSystem

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	apomiticSystem
Definition	The general mode of asexual reproduction through seeds of a plant species.
Comments	In absence or presence, but unknown, apomictic system the value should be filled according (absence, unknown)
Examples	gametophytic, absent, unknown
Controlled vocabulary	present, absent, gametophytic, sporophytic, autonomous, pseudogamy, facultative, obligatory
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

styleLength

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	styleLength
Definition	The average length from the base to the tip of the style(s) of flower(s) of this plant Occurrence
Comments
Examples	12.5, 6.5, 20.0
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

floralReward

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	floralReward
Definition	A list (concatenated and separated) of rewards offered by flowers to visiting animals in order to award their services.
Comments	Absence of reward applies when flowers are pollinated by deceit (no reward offered to visiting animals). Recommended best practice is to separate the values in a list with space vertical bar space ( | ) and use a controlled vocabulary of floral rewards.
Examples	nectar, pollen | nectar, absence of reward
Controlled vocabulary	nectar, pollen, oil, gum, resin, perfume, floral tissues, other, absence of reward
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

fruitSet

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	fruitSet
Definition	Percentage of flowers exposed to floral visitors during anthesis that set fruit.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

removedPollenGrainsQuantity

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	removedPollenGrainsQuantity
Definition	The number or enumeration value for the quantity of pollen grains removed from the anther(s) of a flower exposed to multiple visitors.
Comments
Examples	156, 350
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

seedSet

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	seedSet
Definition	Number of mature seeds of a fruit from a flower exposed to a single visitor.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

flowerHabit

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	flowerHabit
Definition	The position (in relation to the ground) the open flower is presented to flower visitors.
Comments	Term reference (literature): Faegri and van der Pijl (1979); Willmer (2011); Rech et al. (2014).
Examples	pendent, declined
Controlled vocabulary	pendent; erect; declined;
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

attractiveStructureColor

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	attractiveStructureColor
Definition	The predominant color of the plant's structure which visually attracts the visiting animal.
Comments	"Recommended best practice is to separate the values with space vertical bar space (
Examples	blue, red | yellow, http://purl.obolibrary.org/obo/PATO_0000951
Controlled vocabulary	Phenotype And Trait Ontology
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

pollinate

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	pollinate
Definition	Indicates if the animal touches the reproductive structures (anthers and stigmas) of a flower during the visit (pollination).
Comments	Recommended best practice is to use values which can be converted to boolean (TRUE or FALSE) such as 0/1, true/false, yes/no.
Examples	yes, no, 0, true
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

cospecificPollenGrainsQuantity

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	cospecificPollenGrainsQuantity
Definition	The number or enumeration value for the quantity of coespecific pollen grains deposited on the flower's stigma(s) exposed to multiple visitors at the end of flower anthesis
Comments
Examples	356, 500
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

resourceCollected

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	resourceCollected
Definition	A list (concatenated and separated) of floral resources used or removed by an animal from a flower during an Interaction.
Comments	Recommended best practice is to separate the values in a list with space vertical bar space ( `
Examples	pollen, pollen | nectar | oil, ovules
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

floralAdvertisement

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	floralAdvertisement
Definition	A list (concatenated and separated) of structures and substances that function advertising the flowers (and its rewards) to floral visitors. Usually as visual, olfactory and tactile stimuli.
Comments	Term reference (literature): Willmer et al. 2011
Examples
Controlled vocabulary	colored structure; presence of perfume (diurnal); presence of perfume (nocturnal); presence of osmophores
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

fertilizedOvulesQuantity

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	fertilizedOvulesQuantity
Definition	The number or enumeration value for the quantity of fertilized ovules in a flower which the Interaction was recorded.
Comments	Should be filled with the number of pollen tubes growing in the style and fertilizing ovules after one visit.
Examples
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

cospecificPollenGrainsQuantitySingleVisit

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	cospecificPollenGrainsQuantitySingleVisit
Definition	The number or enumeration value for the quantity of coespecific pollen grains deposited on the flower's stigma(s) exposed to a single visitor at the end of flower anthesis.
Comments
Examples	223, 100
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

removedPollenGrainsQuantitySingleVisit

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	removedPollenGrainsQuantitySingleVisit
Definition	The number or enumeration value for the quantity of pollen grains removed from the anther(s) of a flower exposed to a single visitor.
Comments
Examples	243, 550
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

flowerOpeningPeriod

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	flowerOpeningPeriod
Definition	The period of the day which a sample of chasmogamous flowers' buds open their corolla, exposing the reproductive parts to flower visitors.
Comments	Recommended best practice is to use a controlled vocabulary of discrete periods or use a time interval that conforms to ISO 8601:2004(E).
Examples	morning, night, 6:00:00Z/12:30:00Z (the interval between 6am UTC and 12:30pm UTC)
Controlled vocabulary	dawn; dusk; morning; noon; afternoon; night (or option of specifying the day time)
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

collectingBodyPartLength

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	collectingBodyPartLength
Definition	The length in millimeters of the body part used to access the floral resource.
Comments	The collectingBodyPart should be provided in order to access which body part this length is related to.
Examples	12, 100
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

stigmaticArea

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	stigmaticArea
Definition	The total surface area in square millimeters of the stigma(s) of a flower.
Comments
Examples	10, 25
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

attractiveStructure

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	attractiveStructure
Definition	The plant structure which is found to visually attract the visiting animal.
Comments	Recommended best practice is to separate the values (singular) in a list with space vertical bar space (
Examples	bract, bract | petal, http://purl.obolibrary.org/obo/PO_0009032
Controlled vocabulary	Plant Ontology
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

floralSystem

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	floralSystem
Definition	The floral system (morphological, temporal or movement-based mechanism) in which bisexual flowers optimize their reproductive success, through mechanisms that promote self- or cross-pollination.
Comments
Examples	herkogamy, heterostyly, stylar dimorphism
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

accumulatedNectarConcentration

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	accumulatedNectarConcentration
Definition	The concentration of the nectar, in percentage of sugar, accumulated at the end of a flower lifespan which was prevented from visiting
Comments
Examples	10.2, 25
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol

accumlatedNectarVolume

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	accumulatedNectarVolume
Definition	The total volume in microliters of nectar accumulated at the end of a flower lifespan which was prevented from visiting
Comments
Examples	5, 10, 5.5
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol	"The nectar volume should be measured with a micro-syringe or calibrated calipers in flowers at end of its lifespan and prevented from visitation during all the lifespan (e.g. bagged). All the volume produced by the flower should be measured and reported in microliters. Protocol reference: Galetto & Bernadello 2005"

heterospecificPollenGrainsQuantity

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	heterospecificPollenGrainsQuantity
Definition	The number or enumeration value for the quantity of heterospecific pollen grains deposited on the stigma(s) of a flower exposed to multiple visitors.
Comments
Examples	435, 600
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

flowerSexuality

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	flowerSexuality
Definition	The sexuality of the flower which this Interaction was recorded regarding to the presence of both (bisexual) stamens (male organs) and pistils (carpels) (female organs), or unisexual, with only male (staminate flower) or female (pistillate or carpellate flower) functional organs.
Comments
Examples	'bisexual', 'male', 'female'
Controlled vocabulary	bisexual, male, female
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

plantPlaceOfContact

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	plantPlaceOfContact
Definition	A list (concatenated and separated) of places (i.e. structures) in the plant that contacts its interacting partner during an Interaction.
Comments	Recommended best practice is to separate the values in a list with space vertical bar space ( `
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

pollenTubesQuantity

Field	Value
GUID
Rebipp Class	rebipp:InteractionOutcome
Label	pollenTubesQuantity
Definition	The number or enumeration value for the quantity of pollen tubes growing in the style of the flower in which the Interaction was recorded when exposed to multiple visitors.
Comments	Should be filled with the number of pollen grains removed from the anthers after one visit.
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to many
Reference Protocol

antherPollenGrainsQuantity

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	antherPollenGrainsQuantity
Definition	The number of pollen grains (male gametophytes) found in the anther(s) of a flower.
Comments
Examples	1523, 2641, 1146
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to many
Reference Protocol	General guidelines for filling fields: Pollen counting should be estimated in fresh or rehydrated pre-anthetic buds (flower almost opening) to prevent pollen grains loss after anthesis. Protocol 2.2. in Dafni et al. (2005); page 40-41.

flowerLongevity

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	flowerLongevity
Definition	The total period of time in hours comprising the time between flower opening and flower senescence (when floral parts begin to wilt and fall off or the ovary starts to develop into fruit).
Comments	Specify the period of time (options with a period varying from 1h to 72h, number of days or weeks).
Examples	1, 8, 72, 120
Controlled vocabulary
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

flowersVisitedQuantity

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	flowersVisitedQuantity
Definition	The number or enumeration value for the quantity of flowers visited in this Interaction.
Comments
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

pollenTubesQuantitySingleVisit

Field	Value
GUID
Rebipp Class	rebipp:FlowerTrait
Label	pollenTubesQuantitySingleVisit
Definition	The number or enumeration value for the quantity of pollen tubes growing in the style of the flower in which the Interaction was recorded when exposed to a single visitor.
Comments	Should be filled with the number of pollen tubes growing in the style after a period of multiple visits.
Examples	2, 4, 10
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

animalPlaceOfContact

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	animalPlaceOfContact
Definition	A list (concatenated and separated) of places (i.e. body parts) of the animal body that contacts its interacting partner during an Interaction.
Comments	Recommended best practice is to separate the values in a list with space vertical bar space ( `
Examples
Controlled vocabulary
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol

caste

Field	Value
GUID
Rebipp Class	rebipp:AnimalTrait
Label	caste
Definition	The society division that is specialized in the function it performs and distinguished by anatomical or morphological differences from other individuals of the society
Comments	Best pratices is to use a controlled vocabulary
Examples	soldier, queen , worker
Controlled vocabulary	soldier, queen , worker
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

antherDehiscenceType

Field	Value
GUID
Rebipp Class	rebipp:PlantTrait
Label	antherDehiscenceType
Definition	The physical mechanism of anther dehiscence (release of the pollen grains) of the recorded plant species.
Comments	Recommended best practice is to use a controlled.
Examples	poricidal, longitudinal
Controlled vocabulary	longitudinal, poricidal, transverse, valvular
Darwin Core Class	Occurrence
Cardinality	One to one
Reference Protocol

verticalStratum

Field	Value
GUID
Rebipp Class	rebipp:Interaction
Label	verticalStratum
Definition	The vertical layering (i.e. stratum) of a habitat where the Interaction occurs.
Comments	Recommended best practice is to use a controlled vocabulary.
Examples	canopy, understory, forest floor
Controlled vocabulary	canopy, subforest, herbaceous stratum
Darwin Core Class	Event
Cardinality	One to one
Reference Protocol