Use cases

Use Cases - not completed!

This page is intent to describe the most common use cases of species/biotic/biological/interspecific interactions.

• Plant-Pollinator Interaction
  • General use case for plant-pollinator interactions
  • Plant-pollinator interactions with associated measurements
• Interaction from e-DNA data

Plant-Pollinator Interactions

This example illustrate the use case for standardization of plant-pollinator interactions dataset.

General use case for plant-pollinator interactions

It is very common in plant-pollinator interaction studies to record the visitation frequencies, number of flowers available to floral visitors and many other measurements which describe the interaction and the interacting organisms.

Dataset source: CaraDonna, P.J. 2020. Temporal variation in plant-pollinator interactions, Rocky Mountain Biological Laboratory, CO, USA, 2013 - 2015 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/27dc02fe1655e3896f20326fed5cb95f (Accessed 2021-05-18).

Dataset description: the dataset contains the plant-pollinator interaction data collected by Paul CaraDonna et al. at the Rocky Mountain Biological Laboratory in Gothic, CO, USA during the 2013, 2014 and 2015 growing season. These data were collected to investigate temporal variation in plant-pollinator interactions; specifically, these data were collected in a manner to allow for the construction of weekly plant-pollinator interaction networks in order to investigate fine scale temporal variation in plant-pollinator interactions. The data represent extensive community-wide field observations of animal pollinators visiting flowering plants in a subalpine ecosystem for the majority of the summer growing season (May–September).

Data sample:

year	date	day_of_year	week_num	site	transect	start_time	end_time	plant	pollinator	interactions	pollinator_family	pollinator_group	pollinator_sex	pollinator_2013	observer
2013	2013-07-11	192	8	shady_point	2	14:35:00	14:50:00	agoceris_aurantiaca	nymphalidae_spp	1	nymphalidae	butterfly	NA	nymphalidae_spp	JLC_PJC
2013	2013-07-18	199	9	shady_point	1	11:15:00	11:25:00	agoceris_aurantiaca	nymphalidae_spp	1	nymphalidae	butterfly	NA	nymphalidae_spp	JLC_PJC
2013	2013-05-31	151	2	twin_meadows	1	11:30:00	11:45:00	androsace_septentrionalis	andrena_cyanophila	2	andrenidae	bee	worker	andrena_cyanophila	JLC_PJC

This data sample was modified from the original dataset

Standardization:

Each row in the dataset includes an interaction between two individuals (a plant and a floral-visitor/pollinator). The interactions are represented as a dwc:Event, since it is an action that occurs at some location during some time, as follow:

File: interactions.csv

eventID	year	eventDate	startDayOfYear	eventTime
evt_1	2013	2013-07-11	192	14:35:00Z/14:50:00Z
evt_2	2013	2013-07-18	199	11:15:00Z/11:25:00Z
evt_3	2013	2013-05-31	151	11:30:00Z/11:45:00Z

The occurrences of are documented in separated file (occurrences.csv) using terms from dwc:Occurrence class, and they are linked to the interactions (a.k.a dwc:Event) using the same dwc:eventID value.

File: occurrences.csv

eventID	occurrenceID	recordedBy	scientificName	family	taxonRank
evt_1	occ_1	JLC_PJC	Agoceris aurantiaca		species
evt_1	occ_2	JLC_PJC	Nymphalidae	Nymphalidae	family
evt_2	occ_3	JLC_PJC	Agoceris aurantiaca		species
evt_2	occ_4	JLC_PJC	Nymphalidae	Nymphalidae	family
evt_3	occ_5	JLC_PJC	Androsace septentrionalis		species
evt_3	occ_6	JLC_PJC	Andrena cyanophila	Andrenidae	species

In the above example occurrences which share the same dwc:eventID participate in the same interaction. But it does not document the direction and the type of the interaction. For this reason, we need to use dwc:ResourceRelatinship linked to each dwc:Event as follow:

File: resource_relationship.csv:

eventID	resourceRelationshipID	resourceID	relatedResourceID	relationshipOfResource	relationshipAccordingTo
evt_1	rr_1	occ_1	occ_2	flowersVisitedBy	JLC_PJC
evt_2	rr_2	occ_3	occ_4	flowersVisitedBy	JLC_PJC
evt_3	rr_3	occ_5	occ_6	flowersVisitedBy	JLC_PJC

It is recommended to use a controlled vocabulary for dwc:relationshipOfResource and for interactions terms can be imported from Relation Ontology.

Plant-pollinator interactions with associated measurements

A very common use case is to associate a number of measurements or facts to each interaction record (e.g. visitation frequency, collected resource, interaction strength). In those cases, we can use dwc:MeasurementOrFact to document this measurements/facts by linking one or many dwc:MeasurementOrFact to the each dwc:Event that we want to describe in more details.

File: measurements.csv

eventID	measurementID	measurementType	measurementValue	measurementUnit
evt_1	m_1	number of visits	1	visits
evt_2	m_2	number of visits	1	visits
evt_3	m_3	number of visits	2	visits

Another common use case is when the measurements or facts are about the dwc:Occurrence's instead about the interactions (dwc:Event). In those cases, we need to use another DwC extension which allows linking both the dwc:Event and the dwc:Occurrence, like obis:ExtendedMeasurementOrFact. The obis:ExtendedMeasurementOrFactt extension introduces new terms to the dwc:MeasurementOrFact making possible to convert the star schema of DwC-Archives into a virtual snowflake schema. Thus, we can use dwc:occurrenceID included in the obis:ExtendedMeasurementOrFact to link measurements or facts to the dwc:Occurrence's and also to the interactions (dwc:Event).

If we have measurements for the interactions and for the occurrences, then we can use obis:ExtendedMeasurementOrFact to document both level of measurements. Otherwise, we have to add a new table to the dataset (e.g. emof.csv).

Since in this example we have measurements for the interactions (number of visits) and for the occurrences (caste, originally documented as pollinator_sex) we can use obis:ExtendedMeasurementOrFact to document both levels of measurements, like it is shown bellow. File: measurements.csv

eventID	occurrenceID	measurementID	measurementType	measurementValue	measurementUnit
evt_1		m_1	number of visits	1	visits
evt_2		m_2	number of visits	1	visits
evt_3		m_3	number of visits	2	visits
evt_3	occ_6	m_4	caste	worker

In the above table the records where the term dwc:occurrenceID are empty indicate that these are measurements or facts of the interactions, on other hand, records with non-empty dwc:occurrenceID document measurements or facts of the dwc:Occurrence's, like the measurement m_3 which documents that the caste of the floral-visitor/pollinator with dwc:occurrenceID equals to occ_6 is a worker.

e-DNA

Some paragraph

Dataset source: Meyer, Jordana M.; Leempoel, Kevin; Losapio, Gianalberto; Hadly, Elizabeth A. (2020): Data_Sheet_1_Molecular Ecological Network Analyses: An Effective Conservation Tool for the Assessment of Biodiversity, Trophic Interactions, and Community Structure.xlsx. Frontiers. Dataset. https://doi.org/10.3389/fevo.2020.588430.s001

Dataset description

Data samples

Standardization