General informations

The data specification is implemented as a collection of JSON schemes, that can be downloaded from the GitHub repository of the project.

For each object, the name of the fields, the type of the field, and additional informations are given. When using the rmangal package, the same information can be viewed using:

api = mangalapi()
whatIs(api, 'taxa')

Note also that when data are uploaded through the R package, (i) the owner field is always set automatically, and (ii) instead of giving URI of the resources, users should give the id, or the list representation of the object directly.

All fields whose type is related are references to other objects in the database. When listing or getting data, these fields will be exposed as their id, primarily because it is a more compact notation for end-users (i.e. /api/v1/taxa/1 will simply be 1). However (expect when using the R package), when adding data, these fields should contain the URI of the resource being linked to.

List of schemes

interaction

units_t

Description Units in which the interaction strength is measured

Data type string

owner

Description Who uploaded the data. URI of the data owner.

Data type related (to_one)

units_f

Description Units in which the interaction strength is measured

Data type string

id

Description Integer data. Ex: 2673

Data type integer

strength_t

Description The strength of the interaction for the item RECEVING the interaction

Data type float

environment

Description List of identifiers (or URIs) of the environments associated to the interaction.

Data type related (to_many)

strength_f

Description The strength of the interaction for the item ESTABLISHING the interaction

Data type float

papers

Description List of identifiers (or URIs) of the references to the papers associated with the dataset.

Data type related (to_many)

latitude

Description Latitude

Data type string

public

Description Whether the interaction can be viewed by all users

Data type boolean

link_type

Description The type of interaction

Data type string

Accepted values predation herbivory ectoparasitism endoparasitism intra-cellular parasitism parasitoidism mycoheterotrophy antixenosis teletoxy amensalism antibiosis allelopathy competition facilitation refuge creation inquilinism phoresis epibiosis pollination mutualistic symbiosis zoochory mutual protection

stage_from

Description The stage of the establishing entity, to be selected in the list of allowed values

Data type string

Accepted values seed juvenile adult dead larva all

description

Description A description of the interaction

Data type string

date

Description The time at which the interaction was sampled

Data type datetime

data

Description List of identifiers (or URIs) of the references describing the data.

Data type related (to_many)

sex_to

Description The sex of the receiving entity, to be selected in the list of allowed values

Data type string

Accepted values all male female unknown

taxa_to

Description Identifier (or URI) of the taxa receiving the interaction.

Data type related (to_one)

item_from

Description Identifier (or URI) of the item establishing the interaction.

Data type related (to_one)

longitude

Description Longitude

Data type string

stage_to

Description The stage of the receiving entity, to be selected in the list of allowed values

Data type string

Accepted values seed juvenile adult dead larva all

item_to

Description Identifier (or URI) of the item receiving the interaction.

Data type related (to_one)

obs_type

Description How the interaction was observed

Data type string

Accepted values unspecified observation litterature absence inferred

taxa_from

Description Identifier (or URI) of the taxa establishing the interaction.

Data type related (to_one)

sex_from

Description The sex of the establishing, to be selected in the list of allowed values

Data type string

Accepted values all male female unknown

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

network

description

Description A short description of the network

Data type string

interactions

Description List of identifiers (or URIs) of the interactions in the network.

Data type related (to_many)

owner

Description A single related resource. Can be either a URI or set of nested resource data.

Data type related (to_one)

longitude

Description Longitude

Data type string

public

Description Whether the network can be viewed by all users

Data type boolean

environment

Description List of identifiers (or URIs) of environmental measurements associated to the network.

Data type related (to_many)

latitude

Description Latitude

Data type string

papers

Description List of identifiers (or URIs) of the references to the papers associated with the dataset.

Data type related (to_many)

date

Description The time at which the network was sampled

Data type datetime

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

data

Description List of identifiers (or URIs) of the references describing the data.

Data type related (to_many)

id

Description Integer data. Ex: 2673

Data type integer

name

Description The name of the network

Data type string

taxa

status

Description The taxonomic status of the taxa.

Data type string

Accepted values confirmed trophic species morphospecies nomen dubium nomen oblitum nomen nudum nomen novum nomen conservandum species inquirenda

tsn

Description The TSN identifier

Data type integer

name

Description The scientific name of the taxa

Data type string

gbif

Description The GBIF identifier of the taxa

Data type integer

description

Description A short description of the taxa

Data type string

ncbi

Description The NCBI Taxonomy identifier of the taxa

Data type integer

eol

Description The EOL identifier of the taxa

Data type integer

traits

Description A list of traits values indentifiers (or URIs) that were measured on this taxa. Good for taxa-level traits.

Data type related (to_many)

vernacular

Description The vernacular name of the taxa, in English

Data type string

owner

Description URI of the taxa owner. When submitting from the R package, this field is populated automatically.

Data type related (to_one)

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

id

Description Integer data. Ex: 2673

Data type integer

bold

Description The BOLD identifier of the taxa

Data type integer

trait

units

Description Units in which the trait was measured

Data type string

name

Description The name of the measured trait

Data type string

owner

Description A single related resource. Can be either a URI or set of nested resource data.

Data type related (to_one)

longitude

Description Longitude

Data type string

latitude

Description Latitude

Data type string

value

Description The value of the trait

Data type string

date

Description The time at which the traits were measured

Data type datetime

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

id

Description Integer data. Ex: 2673

Data type integer

description

Description A longer description of the trait

Data type string

dataset

description

Description A short description of the dataset

Data type string

id

Description Integer data. Ex: 2673

Data type integer

environment

Description List of identifiers (or URIs) of the environments associated to the dataset.

Data type related (to_many)

public

Description Whether the dataset can be viewed by all users

Data type boolean

papers

Description List of identifiers (or URIs) of the references to the papers associated with the dataset.

Data type related (to_many)

owner

Description A single related resource. Can be either a URI or set of nested resource data.

Data type related (to_one)

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

data

Description List of identifiers (or URIs) of the references describing the data.

Data type related (to_many)

networks

Description List of identifiers (or URIs) of the networks in the dataset.

Data type related (to_many)

name

Description The name of the dataset

Data type string

environment

description

Description A description of the environmental property

Data type string

value

Description The value of the environmental property

Data type string

name

Description The environmental property being measured

Data type string

units

Description The units in which the environmental property is measured

Data type string

owner

Description A single related resource. Can be either a URI or set of nested resource data.

Data type related (to_one)

id

Description Integer data. Ex: 2673

Data type integer

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string

item

units

Description Units in which the population size is measured

Data type string

description

Description A short description of the population

Data type string

level

Description Whether the item is a single individual, or a population

Data type string

Accepted values individual population

taxa

Description The identifier (or URI) of the taxa object to which the item belongs.

Data type related (to_one)

name

Description A name for the item, useful to identify it later

Data type string

traits

Description A list of traits values indentifiers (or URIs) that were measured on this item.

Data type related (to_many)

owner

Description A single related resource. Can be either a URI or set of nested resource data.

Data type related (to_one)

size

Description If the item is a population, the number of individuals or biomass

Data type float

id

Description Integer data. Ex: 2673

Data type integer

resource_uri

Description Unicode string data. Ex: "Hello World"

Data type string