*mandatory fields

Name Controlled vocabullary Description Value format
* nameName of the sample
* sample_nameIdentical to sample name in "eLMSG_v5.0_MAG.xlsx" for relating the sample information to the according genome sequence.
* organismThe most descriptive scientific name for the sample (to the species, if possible). You can refer to the NCBI taxonomy database (https://www.ncbi.nlm.nih.gov/). In the case of a new species, please contact node-support@picb.ac.cn. The corresponding organism of human is Homo sapiens.
descriptionDescription of the sample
collect_dateThe date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 1990-10-30, 1990-10, 2015-10-11T17:53:03Z
biomaterial_providerName and address of the lab or PI, or a culture collection identifier
treatmentThe processing of samples or sample processing protocol.
sample_loc Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"
* env_biomeDescriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
* env_packageCVEnvironmental package MIGS/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.air | host-associated | human-associated | human-gut | human-oral | human-skin | human-vaginal | microbial mat/biofilm | miscellaneous natural or artificial environment | plant-associated | sediment | soil | wastewater/sludge | water | built_ environment
* biomeCVFive-tiered metagenome classification, Ecosystem:Ecosystem Category:Ecosystem Type:Ecosystem Subtype:Specific Ecosystem. If your sample biome is not in the list, you can add it according to the rules of biome
altitudeThe altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.
water_depthWater depth is defined as the vertical distance below the surface of the water
depth_below_surfaceDepth below surface is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth below surface can be reported as an interval for subsurface samples.
lat_lonThe geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.ddddd] N|S d[dd.ddddd] W|E", eg, 38.98000 N 77.11000 W
elevationThe elevation of the sampling site as measured by the vertical distance from mean sea leve, number:unit
latitude_startThe geographical coordinates of the location where the sample was collected. Specify as degrees latitude starting in format "d[d.ddddd] N|S", eg, 38.98000 N
latitude_endThe geographical coordinates of the location where the sample was collected. Specify as degrees latitude ending in format "d[dd.ddddd] N|S", eg, 40.13000 N
longtitude_startThe geographical coordinates of the location where the sample was collected. Specify as degrees longitude strating in format "d[dd.ddddd] W|E", eg, 77.11000 W
longtitude_endThe geographical coordinates of the location where the sample was collected. Specify as degrees longitude strating in format "d[dd.ddddd] W|E", eg, 78.11000 W
samp_collect_deviceThe method or device employed for collecting the sample, e.g. biopsy, niskin bottle, push core
temperatureEnvironmental temperature of the sample at time of sampling
env_oxygenOxygenation status of sample
env_salinitySalinity measurement
env_nitrogen_totTotal nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
env_phosphate_totTotal amount or concentration of phosphate
env_phosphorus_totTotal phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus
env_phosphateTotal amount or concentration of phosphate
env_nitrateConcentration of nitrate
env_nitriteConcentration of nitrite
nitrogen_isotopic_informationDescription of measured nitrogen isotopic infromation
env_chlorophyllConcentration of chlorophyll
env_alkalinityAlkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
env_ammoniumConcentration of ammonium
env_chlorideConcentration of chloride
env_sulfateConcentration of sulfate
env_sulfideConcentration of sulfide
sulfur_isotopic_informationDescription of measured sulfur isotopic infromation
env_diss_org_carbConcentration of dissolved organic carbon
env_part_org_carbConcentration of particulate organic carbon
env_part_inorg_carbConcentration of particulate inorganic carbon, eg 8 mg/L
carbon_isotopic_infromationDescription of measured carbon isotopic infromation
methaneConcentration of methane, eg 2 mM
description_of_alkanes_concentrationThe concentration of other alkanes if measured
total_ironConcentration of iron, eg 10 mg/L
ferrous_ironConcentration of ferrous iron, eg 2 mM
calcium_ionConcentration of calcium iron, eg 6 mM
magnesium_ionConcentration of magnesium iron, eg 10 mM
env_diss_oxygenConcentration of dissolved oxygen
env_phaeopigmentsConcentration of phaeopigments; can include multiple phaeopigments
env_phpH measurement
env_pressurePressure to which the sample is subject, in atmospheres
env_ref_biomaterialPrimary publication if isolated before genome publication; otherwise, primary genome report
env_source_mat_idA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
rel_to_oxygenCVIs this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environmentsaerobe | anaerobe | facultative | microaerophilic | microanaerobe | obligate aerobe | obligate anaerobe
env_samp_processAny processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI
env_gaseous_substancesAmount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
env_pre_treatmentThe process of pre-treatment removes materials that can be easily collected from the raw wastewater
env_samp_vol_we_dna_extVolume (mL) or weight (g) of sample processed for DNA extraction
env_soluble_inorg_matConcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
midMolecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters.
adaptersAdapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
perturbationType of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types.
storage_typeCVSample storge typefridge | freezer | liquid nitrogen | formalin | paraffin | Other
storage_temperatureCVSample storage temperature4℃ | -20℃ | -80℃ | -195.79℃ | room temperature | 37℃ | 25℃ | fresh
storage_locationSample storage location
protocolDecription of sample processing protocal
extracted_mol_type CVMolecular types extracted from samples, e.g. total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, genomic DNA, protein, etc.total RNA | polyA RNA | cytoplasmic RNA | nuclear RNA | genomic DNA | protein
extraction_reagentReagents used to extract molecules from samples