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Table 3 M2B3 Reporting Standard about a sample

From: Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

 

Descriptor name

Description of usage

Control vocabulary/format/unit

Example

 

SAMPLE_Title

A short informative description of the sample. Must be unique for each sample, (i.e. for each filter generated during sampling).

Format: <OSD_SiteID > _ < Month > _ < Year > _ < SiteName > _ < Protocol_Label > _ < SampleNo > _ < Depth>

OSD3_06_14_Helgoland_NPL022_1_surface

 

SAMPLE_Depth

The distance below the surface of the water at which a measurement was made or a sample was collected.

Format: ##.#;

1.5

Positive below the sea surface.

SDN:P06:46:ULAA for m

SAMPLE_Protocol_Label

Identifies the protocol used to produce the sample, e.g. filtration and preservation.

Term list;

NPL022

See the SAMPLE_Protocol_Label in the OSD Protocols Section for details

SAMPLE_Quantity

Refers to the quantity of environment that was sampled, most often with dimensions Length, Amount, Mass or Time.

Format : ###.###

20 Litres

See the SAMPLE_Quantity in the OSD Protocols Section for details

SAMPLE_Container

Refers to the container in which the sample is stored prior to analysis.

Term list;

Sterivex cartridge

See the SAMPLE_Container in the OSD Protocols Section for details

SAMPLE_Content

Refers to the content of the sample container. While the sample might target a specific organism (e.g. bacteria), the sample content might be a filter or a volume of water.

Term list;

Particulate matter on a 0.22 μm pore size filter

See the SAMPLE_Content in the OSD Protocols Section for details

SAMPLE_Size-Fraction_Upper-Threshold

Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample.

Term list;

no pre-filtration

See the SAMPLE_Size-Fraction_Upper-Threshold in the OSD Protocols Section for details; in μm

SAMPLE_Size-Fraction_Lower-Threshold

Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are exclude from the sample.

Term list;

0.22

See the SAMPLE_Size-Fraction_Lower-Threshold in the OSD Protocols Section for details; in μm

SAMPLE_Treatment_Chemicals

Refers to the chemicals (e.g. preservatives) added to the sample.

Terms list: ChEBI;

None

See the SAMPLE_Treatment_Chemicals in the OSD Protocols Section for details

SAMPLE_Treatment_Storage

Refers to the conditions in which the sample is stored, e.g. temperature, light conditions, time.

Term list;

−80 degrees Celsius

See the SAMPLE_Treatment_Storage in the OSD Protocols Section for details

  1. Mandatory information is in bold and other fields are recommended. OSD Protocols are available at http://www.microb3.eu/sites/default/files/osd/OSD_Handbook_v2.0.pdf. ChEBI is an ontological classification and dictionary of small chemical compounds (http://www.ebi.ac.uk/chebi/init.do).