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José Augusto Salim edited this page May 18, 2021 · 2 revisions

Use Cases - not completed!

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

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

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