ARMS 2018 dataset on long-term monitoring and biodiversity assessment of invasive and indigenous hard-bottom communities

The ARMS-MBON (Marine Biodiversity Observation network for genetic monitoring of hard-bottom communities) European project is a Genomics Observatory and a collaboration of ~25 European institutes who deploy individual settlement units in the vicinity of marine stations and Long-term Ecological Research sites in European coastal waters and Antarctica. After a few months they are brought up, and visual, photographic, and genetic assessments are made of the lifeforms that settled on them. These data will be used to assess the status of, and changes in, the hard-bottom communities of these near-coast environments. This project began collecting full scientific data in 2019.

This dataset linked to this record contains the ARMS data of 2018. Note that this dataset is not yet complete and will undergo several updates. In the "MasterARMS" file you can find the data collected during the sampling, links to images of the ARMS plates, the run accession codes of the sequences in ENA, and access status (open or closed). The documentation you can download are the various SOPs. The "MasterARMS" file and documentation are open access, but some of the images and sequences are subject to a moratorium period.

Default

Identification

Alternate Identifier

e6289cf6-dde7-4584-89e6-bd7e907a4b5f

Publication Date
2020-04-01
Title

ARMS 2018 dataset on long-term monitoring and biodiversity assessment of invasive and indigenous hard-bottom communities

Short Name

MasterARMS.csv

Abstract

The ARMS-MBON (Marine Biodiversity Observation network for genetic monitoring of hard-bottom communities) European project is a Genomics Observatory and a collaboration of ~25 European institutes who deploy individual settlement units in the vicinity of marine stations and Long-term Ecological Research sites in European coastal waters and Antarctica. After a few months they are brought up, and visual, photographic, and genetic assessments are made of the lifeforms that settled on them. These data will be used to assess the status of, and changes in, the hard-bottom communities of these near-coast environments. This project began collecting full scientific data in 2019.

This dataset linked to this record contains the ARMS data of 2018. Note that this dataset is not yet complete and will undergo several updates. In the "MasterARMS" file you can find the data collected during the sampling, links to images of the ARMS plates, the run accession codes of the sequences in ENA, and access status (open or closed). The documentation you can download are the various SOPs. The "MasterARMS" file and documentation are open access, but some of the images and sequences are subject to a moratorium period.

Dataset Language

eng

 
Dataset Creator
Metadata Provider
Dataset Contact
Keywords (none)

  • Genomics

  • Hard-bottom communities

  • Invasive species

  • Long-term monitoring

  • ARMS

  • IJI

Keywords (Aquatic Sciences and Fisheries Abstracts (ASFA))

  • Marine biology

  • DNA

Geographic Coverage

Geographic Description

Hard-bottom environments in Europe and the (Ant)arctic

Bounding Box

West Bounding Coordinate

11.111884

East Bounding Coordinate

25.136605

North Bounding Coordinate

58.87633

South Bounding Coordinate

35.343153

Temporal Coverage

Range of Dates

Begin Date

2018-04-18

End Date

2019-01-28

Taxonomic Coverage

No information provided.

License Information

Intellectual Rights

CC BY

 

Distribution

Online

A brief description of the the content of online URL.

Dataset

URL
https://mda.vliz.be/directlink.php?fid=VLIZ_00000615_5f4ce393c5d84
 
 

Project

• Project

Title

ASSEMBLE Plus

Abstract

Association of European Marine Biological Laboratories Expanded: http://www.assembleplus.eu/

Personnel

Organization Name

ASSEMBLE Plus

Individual Name

Given Name

None

Surname

None

Position Name

None

 
 

Methods

• Method

Method Step

Description

The Standard Operating Procedures for the sampling and sample pre-processing, as documented in the ARMS Handbook and relevant for the ARMS data of 2018

Citation

The ARMS Handbook, 2020, ARMS consortium, http://www.assembleplus.eu/sites/assembleplus.eu/files/public/ARMS/ARMS_Handbook.pdf

Method Step

Description

The Molecular Standard Operating Procedures, for DNA extraction and PCR amplification and sequencing and relevant for the ARMS data of 2018

Citation

The ARMS MSOPs, 2020, ARMS consortium, http://www.assembleplus.eu/sites/assembleplus.eu/files/public/ARMS/ARMS_MSOPs.pdf

 
 

Data Tables

• Data Table

Name

MasterARMS_2018.csv

Physical

Data Format

Externally Defined Format

Format Name

CSV

Attribute List

Attribute

Name

Country

Label

Country Name

Definition

Name of the Country where the ARMS observsatory is located

Standard Unit

Attribute

Name

ObservatoryID

Label

Collection site

Definition

Location of the ARMS observatory

Standard Unit

Attribute

Name

ARMSID

Label

ARMS observatory code

Definition

Code (unique identifier) of the ARMS observatory

Standard Unit

Attribute

Name

MaterialSampleID

Label

Sample identifier

Definition

Unique sample identifier containing information about observatoryID, ARMSID, deployment date, collection date and abbreviation of sample specification (i.e. fraction, preservative, filter, etc...)

Standard Unit

Attribute

Name

longitude

Label

Longitude

Definition

Collection site longitude

Standard Unit

Decimal degree

Attribute

Name

latitude

Label

Latitude

Definition

Collection site latitude

Standard Unit

Decimal degree

Attribute

Name

depth

Label

Depth

Definition

Collection site depth

Standard Unit

Meter

Attribute

Name

Deploy_Date

Label

Deployment Date

Definition

Date of ARMS unit deployment

Standard Unit

DD/MM/YYYY

Attribute

Name

Collect_Date

Label

Collection Date

Definition

Date of ARMS unit collection

Standard Unit

DD/MM/YYYY

Attribute

Name

physicalSampleID

Label

Physical sample identifier

Definition

The sampleID as written on the falcon tubes containing the material to be sequences. It should be equal to MaterialSampleID.

Standard Unit

Attribute

Name

Fraction

Label

Sampling fraction

Definition

Description of the sampling fraction (i.e. sessile, motile, sediment, plankton, images)

Standard Unit

Attribute

Name

Preservative

Label

Preservation method

Definition

Preservation method used for each fraction (i.e. EtOH, DMSO, frozen)

Standard Unit

Attribute

Name

Filter

Label

Filter size

Definition

Filter pore size used to select the sampling fraction

Standard Unit

Micrometer

Attribute

Name

gene_COI

Label

Accession number COI gene

Definition

ENA (European Nucleotide Archive) run accession number of COI gene

Standard Unit

ENA run accession number

Attribute

Name

gene_18S

Label

Accession number 18S gene

Definition

ENA (European Nucleotide Archive) run accession number of 18S gene

Standard Unit

ENA run accession number

Attribute

Name

gene_ITS

Label

Accession number ITS gene

Definition

ENA (European Nucleotide Archive) run accession number of ITS gene

Standard Unit

ENA run accession number

Attribute

Name

negativeControl_gene_COI

Label

Accession number negative control of COI gene

Definition

ENA (European Nucleotide Archive) run accession number of negative control used for COI gene

Standard Unit

ENA run accession number

Attribute

Name

negativeControl_gene_18S

Label

Accession number negative control of 18S gene

Definition

ENA (European Nucleotide Archive) run accession number of negative control used for 18S gene

Standard Unit

ENA run accession number

Attribute

Name

negativeControl_gene_ITS

Label

Accession number negative control of ITS gene

Definition

ENA (European Nucleotide Archive) run accession number of negative control used for ITS gene

Standard Unit

ENA run accession number

Attribute

Name

OtherData_m2mlink

Label

Machine to machine URL to the dataset

Definition

It is the URL to the associated dataset (either images or CVS files) that a machine to machine connection should use since it results in an immediate download.

Standard Unit

Attribute

Name

OtherData_humanLink

Label

Human URL to the dataset

Definition

It is the URL to the associated dataset (either images or CVS files) that a user can use since it links to a metadata sheet where there is a download button.

Standard Unit

Attribute

Name

OpenAccess

Label

Data availability

Definition

Specify if data are open access.

Standard Unit