LifeWatch ERIC Metadata Catalogue
ARMS 2018 dataset on long-term monitoring and biodiversity assessment of invasive and indigenous hard-bottom communities
Short name: MasterARMS.csv.
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
- Abstract
-
Short name: MasterARMS.csv.
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
License Information
- Intellectual Rights
- CC BY
Resource License
- License Name
- Creative Commons
Distribution
Online
- A brief description of the the content of online URL.
Project
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
Methods
Methods
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 Table
Data Table
Data Table
- Name
- MasterARMS_2018.csv
Physicaldocument
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
