| * name | | Name of the sample | |
| * sample_name | | Identical to sample name in "eLMSG_v5.0_MAG.xlsx" for relating the sample information to the according genome sequence. | |
| * organism | | The 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. | |
| description | | Description of the sample | |
| related_links | | | |
| collect_date | | The 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_provider | | Name and address of the lab or PI, or a culture collection identifier | |
| treatment | | The 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_biome | | Descriptor 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_package | CV | Environmental 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 |
| * biome | CV | Five-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 | |
| altitude | | The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air. | |
| water_depth | | Water depth is defined as the vertical distance below the surface of the water | |
| depth_below_surface | | Depth 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_lon | | The 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 | |
| elevation | | The elevation of the sampling site as measured by the vertical distance from mean sea leve, number:unit | |
| latitude_start | | The 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_end | | The 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_start | | The 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_end | | The 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_device | | The method or device employed for collecting the sample, e.g. biopsy, niskin bottle, push core | |
| temperature | | Environmental temperature of the sample at time of sampling | |
| env_oxygen | | Oxygenation status of sample | |
| env_salinity | | Salinity measurement | |
| env_nitrogen_tot | | Total 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_tot | | Total amount or concentration of phosphate | |
| env_phosphorus_tot | | Total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus | |
| env_phosphate | | Total amount or concentration of phosphate | |
| env_nitrate | | Concentration of nitrate | |
| env_nitrite | | Concentration of nitrite | |
| nitrogen_isotopic_information | | Description of measured nitrogen isotopic infromation | |
| env_chlorophyll | | Concentration of chlorophyll | |
| env_alkalinity | | Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate | |
| env_ammonium | | Concentration of ammonium | |
| env_chloride | | Concentration of chloride | |
| env_sulfate | | Concentration of sulfate | |
| env_sulfide | | Concentration of sulfide | |
| sulfur_isotopic_information | | Description of measured sulfur isotopic infromation | |
| env_diss_org_carb | | Concentration of dissolved organic carbon | |
| env_part_org_carb | | Concentration of particulate organic carbon | |
| env_part_inorg_carb | | Concentration of particulate inorganic carbon, eg 8 mg/L | |
| carbon_isotopic_infromation | | Description of measured carbon isotopic infromation | |
| methane | | Concentration of methane, eg 2 mM | |
| description_of_alkanes_concentration | | The concentration of other alkanes if measured | |
| total_iron | | Concentration of iron, eg 10 mg/L | |
| ferrous_iron | | Concentration of ferrous iron, eg 2 mM | |
| calcium_ion | | Concentration of calcium iron, eg 6 mM | |
| magnesium_ion | | Concentration of magnesium iron, eg 10 mM | |
| env_diss_oxygen | | Concentration of dissolved oxygen | |
| env_phaeopigments | | Concentration of phaeopigments; can include multiple phaeopigments | |
| env_ph | | pH measurement | |
| env_pressure | | Pressure to which the sample is subject, in atmospheres | |
| env_ref_biomaterial | | Primary publication if isolated before genome publication; otherwise, primary genome report | |
| env_source_mat_id | | A 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_oxygen | CV | Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments | aerobe | anaerobe | facultative | microaerophilic | microanaerobe | obligate aerobe | obligate anaerobe |
| env_samp_process | | Any 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_substances | | Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances | |
| env_pre_treatment | | The process of pre-treatment removes materials that can be easily collected from the raw wastewater | |
| env_samp_vol_we_dna_ext | | Volume (mL) or weight (g) of sample processed for DNA extraction | |
| env_soluble_inorg_mat | | Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. | |
| mid | | Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters. | |
| adapters | | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters | |
| perturbation | | Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types. | |
| storage_type | CV | Sample storge type | fridge | freezer | liquid nitrogen | formalin | paraffin | Other |
| storage_temperature | CV | Sample storage temperature | 4℃ | -20℃ | -80℃ | -195.79℃ | room temperature | 37℃ | 25℃ | fresh |
| storage_location | | Sample storage location | |
| storage_duration | | | |
| protocol | | Decription of sample processing protocal | |
| extracted_mol_type | CV | Molecular 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_reagent | | Reagents used to extract molecules from samples | |
