MIxS Checklist · ERC000030
Minimum information about a Tara Oceans sample. A checklist for reporting metadata of oceanic plankton samples associated with genomics data from the Tara Oceans Expedition.
event_labelAn Event corresponds to the deployment of a sampling device. It is bound in space and time. The Event Label is a unique identifier composed of the project prefix "TARA", sampling date/time "yyyymmddThh:mm:ssZ", station number "000" and a short label to indicate the sampling device used, e.g. "EVENT_CAST", "EVENT_NET", "EVENT_PUMP". Example: TARA_20110416T1508Z_100_EVENT_CAST.
event_datetime_startDate and time in UTC when the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: yyyy-mm-ddThh:mm:ssZ. Example: 2011-04-16T15:05:30Z.
event_datetime_endDate and time in UTC when the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: yyyy-mm-ddThh:mm:ssZ. Example: 2011-04-16T15:38:00Z.
latitude_startLatitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6666.
longitude_startLongitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1012.
latitude_endLatitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6643.
longitude_endLongitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1171.
protocol_labelIdentifies the protocol used to produce the sample, e.g. filtration and preservation. Example: BACT_NUC_W0.22-1.6.
sample_statusRefers to the completness of sample metadata validation. Example: preliminary but can be used to provide data discovery services.
last_update_dateDate of the last update of this sample in the SAMPLES REGISTRY. Example: 2014-03-01Z.
sample_collection_deviceThe device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
sample_storage_deviceThe container used to store the sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device.
sizefraction_lower_thresholdRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
sizefraction_upper_thresholdRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
project_nameName of the project within which the sequencing was organized
environmental_packageMIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
collection_dateThe date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.
broadscale_environmental_contextReport the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
local_environmental_contextReport the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for "broad-scale environmental context". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
environmental_mediumReport the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
sampling_campaignRefers to a finite or indefinite activity aiming at collecting data/samples, e.g. a cruise, a time series, a mesocosm experiment. Example: TARA_20110401Z.
sampling_stationRefers to the site/station where data/sample collection is performed. Example: TARA_100.
sampling_platformRefers to the unique stage from which the sampling device has been deployed. Includes Platform category from SDN:L06, http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=L06, and Platform name. Example: Research Vessel Tara.
marine_regionThe geographical origin of the sample as defined by the marine region name chosen from the Marine Regions vocabulary at http://www.marineregions.org/. Example: Aegean Sea.
salinity_sensorSalinity of water at the time of taking the sample. Format: ##.####, SDN:P02:75:PSAL, SDN:P06:46:UGKG for PSU. Example: 39.2268.
oxygen_sensorOxygen concentration parameters in the water column measured in volts and converted to micromoles per kilogrammes. Format: ###.####, SDN:P02:75:DOXY, SDN:P06:46:KGUM for µmol/kg. Example: 217.7895.
nitrate_sensorNitrate concentration parameters in the water column measured in volts and converted to micromoles per litres. Format: ##.####, SDN:P02:75:NTRA, SDN:P06:46:UPOX for µmol/L. Example: 0.2259.
water_temperatureTemperature of water at the time of taking the sample. Format: ##.####, SDN:P02:75:TEMP, SDN:P06:46:UPAA for °C. Example: 17.7122.
chlorophyll_sensorFluorescence of the water measured in volts and converted to milligrammes of chlorophyll per cubic metre. Format: ##.####, SDN:P02:75:CPWC, SDN:P06:46:UMMC for mg Chl/m3. Example: 0.066.
geographic_location_country_andor_seaThe geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).
citationCitation of the Sample Registry (HTML version) at the PANGAEA. Example: doi.pangaea.de/10.1594/PANGAEA.76752.
further_detailsReference details related to a sample in form of an URI.
depthThe vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.