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Metadata: Genetic sequencing data from Scottish environmental samples and reference cultures 2021
Abstract:
Sequencing data from environmental samples and reference cultures, including paralytic shellfish toxin data and environmental cell counts, published by the Food Standards Scotland as part of the routine monitoring programme.
Data holder:
Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)
| Other details | ||
| Internal code | Internally assigned metadata identifier | 10352 |
| Title | The title is used to provide a brief and precise description of the dataset such as 'Date', 'Originating organisation/programme', 'Location' and 'Type of survey'. All acronyms and abbreviations should be reproduced in full. | Genetic sequencing data from Scottish environmental samples and reference cultures 2021 |
| File Identifier | The File Identifier is a code, preferably a GUID, that is globally unique and remains with the same metadata record even if the record is edited or transferred between portals or tools. | CEFAS9ebd811e-d58e-4912-af9c-2c9f225c8999 |
| Resource Identifier | This is the code assigned by the data owner. | CEFAS21945 |
| Resource type | The resource type will likely be a dataset but could also be a series (collection of datasets with a common specification) or a service. | dataset |
| Start date | This describes the date the resource starts. This may only be the year if month and day are not known | 2021-05-24 |
| End date | This describes the date the resource ends. This may only be the year if month and day are not known | 2021-09-08 |
| Frequency of updates | This describes the frequency with which the resource is modified or updated i.e. a monitoring programme that samples once per year has a frequency that is described as 'annually'. | notPlanned |
| Abstract | The abstract provides a clear and brief statement of the content of the resource. | Sequencing data from environmental samples and reference cultures, including paralytic shellfish toxin data and environmental cell counts, published by the Food Standards Scotland as part of the routine monitoring programme. |
| Lineage | Lineage includes the background information, history of the sources of data, data quality statements and methods. | The samples were collected as part of the routine monitoring programme on behalf of Food Standards Scotland and were done so in accordance with European Union regulations: Regulation (EU) 2019/627 of 15 March 2019 laying down uniform practical arrangements for the performance of official controls on products of animal origin intended for human consumption in accordance with Regulation (EU) 2017/625 of the European Parliament and of the Council and amending Commission Regulation (EC) No 2074/2005 as regards official controls. Analysis of shellfish flesh for paralytic shellfish toxins was performed using pre-column oxidation with fluorescence detection, cell counts were performed on Lugol's fixed water samples in a Sedgwick Rafter settlement chamber. All routine analysis was performed under in accordance with UKAS accreditation. Sequencing was performed on the same Lugol's fixed samples as used for the cell counts and was done using Nanopore sequencing technologies MinION MK 1B and a custom computing device out lined in the link above. In brief, the assay used isothermal amplification to target Alexandrium DNA for sequencing, once generated, the sequencing data were compared to a reference, list providing real time identification of species likely to be present and also the ability to confirm this data using further bio-informatic tools. The data generated for this study and that taken from the routine monitoring programme were anonymised to ensure there is no negative impact harvesters from study areas. The locations are available in the internal data and as such should not be shared externally without removal of site names. The manuscript identifies the sampling sites as follows "The environmental study made use of legacy material collected in 2021 as part of the routine monitoring program by Scottish Association of Marine Science, Oban, Scotland on behalf of Food Standards Scotland". The manuscript is published in MDPI-Toxins: `Toxins | Free Full-Text | Combining Nanopore Sequencing with Recombinase Polymerase Amplification Enables Identification of Dinoflagellates from the Alexandrium Genus, Providing a Rapid, Field Deployable Tool (mdpi.com)`_. Sequencing data generated from the study was compared to the existing (and published) routine monitoring data to see how the assay used could add value to routine monitoring processes. The assay used isothermal amplification to target Alexandrium DNA for sequencing, once data was generated, the resulting sequences were compared to a reference list providing real time identification of species likely to be present and also the ability to confirm this data using further bio-informatic tools. This allowed the rapid low cost an .. _`toxins | free full-text | combining nanopore sequencing with recombinase polymerase amplification enables identification of dinoflagellates from the alexandrium genus, providing a rapid, field deployable tool (mdpi.com)`: https://www.mdpi.com/2072-6651/15/6/372 |
| Related keywords | ||
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Algal bloom |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Aquaculture | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Aquatic environment | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Agricultural and aquaculture facilities | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Habitats and biotopes | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Unknown | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Marine Environmental Data and Information Network | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | data.gov.uk | |
| Geographical coverage | ||
| North | The northern-most limit of the data resource in decimal degrees | 52.4595 |
| East | The eastern-most limit of the data resource in decimal degrees | 1.74086 |
| South | The southern-most limit of the data resource in decimal degrees | 52.4581 |
| West | The western-most limit of the data resource in decimal degrees | 1.73881 |
| Responsible organisations | ||
| Role | The point of contact is person or organisation with responsibility for the creation and maintenance of the metadata for the resource. | pointOfContact |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The originator is the person or organisation who created, collected or produced the resource. | originator |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The custodian is the person or organisation that accepts responsibility for the resource and ensures appropriate care and maintenance. If a dataset has been lodged with a Data Archive Centre for maintenance then this organisation is be entered here. | custodian |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The distributor is the person or organisation that distributes the resource. | distributor |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The owner is the person or organisation that owns the resource. | owner |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| data.manager@cefas.co.uk | ||
| Resource locators | ||
| Locator URL | Web address (URL) that links to the resource | https://data.cefas.co.uk/view/21945 |
| Locator name | Name of the web resource | Cefas Data Portal |
| Dataset constraints | ||
| 20.1 Limitations on Public Access - Access constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 20.2 Limitations on Public Access - Other constraints | noLimitations | |
| 21.1 Conditions for Access and Use - Use constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 21.2 Conditions for Access and Use - Other constraints | http://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_RestrictionCode | |
| Version info | ||
| Date of publication | The publication date of the resource or if previously unpublished the date that the resource was made publicly available via the MEDIN network. | 2024-09-04 |
| Date of last revision | The most recent date that the resource was revised. | 2024-09-24 |
| Date of creation | The date that the resource was created. | 2024-06-07 |
| Harvest date | The date which this record has been (re)harvested from the provider. | 2026-04-19 |
| Metadata date | The date when the content of this metadata record was last updated. | 2024-09-24 |
| Metadata standard name | The name of the metadata standard used to create this metadata | MEDIN |
| Metadata standard version | The version of the MEDIN Discovery Metadata Standard used to create the metadata record | 3.1.1 |