MIMAG.host-associated.6.0 MIMAG: metagenome-assembled genome, host-associated; version 6.0 MIMAG Metagenome-assembled Genome host-associated host-associated wgs_diploid Use for metagenome-assembled genome sequences produced using computational binning tools that group sequences into individual organism genome assemblies starting from metagenomic data sets. Organism cannot contain the term 'metagenome'. Use the MIUVIG package for virus genomes. Before creating BioSamples for prokaryotic and eukaryotic MAGs, please read and follow the MAG submission instructions at https://www.ncbi.nlm.nih.gov/genbank/wgsfaq/#metagen. # This is a submission template for batch deposit of 'MIMAG: metagenome-assembled genome, host-associated; version 6.0' samples to the NCBI BioSample database (https://www.ncbi.nlm.nih.gov/biosample/). # Fields with an asterisk (*) are mandatory. Your submission will fail if any mandatory fields are not completed. If information is unavailable for any mandatory field, please enter 'not collected', 'not applicable' or 'missing' as appropriate. # All other fields are optional. Leave optional fields empty if no information is available. # You can add any number of custom fields to fully describe your BioSamples, simply include them in the table. # CAUTION: Be aware that Excel may automatically apply formatting to your data. In particular, take care with dates, incrementing autofills and special characters like / or -. Doublecheck that your text file is accurate before uploading to BioSample. # TO MAKE A SUBMISSION: # 1. Complete the template table (typically in Excel, or another spreadsheet application) # 2. Save the worksheet as a Text (Tab-delimited) file - use 'File, Save as, Save as type: Text (Tab-delimited)' # 3. Upload the file on the 'Attributes' tab of the BioSample Submission Portal at https://submit.ncbi.nlm.nih.gov/subs/biosample/. # 4. If you have any questions, please contact us at biosamplehelp@ncbi.nlm.nih.gov. isolate isolate identification or description of the specific individual from which this sample was obtained collection date collection_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 "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format {timestamp} broad-scale environmental context env_broad_scale Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.:  mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] {term} local-scale environmental context env_local_scale Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.:  shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] {term} environmental medium env_medium Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] {term} geographic location geo_loc_name Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-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" {term}:{term}:{text} isolation source isolation_source Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. None latitude and longitude lat_lon The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W {float} {float} altitude altitude The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air. {float} m ancestral data ances_data Information about either pedigree or other ancestral information description, e.g., parental variety in case of mutant or selection, A/3*B (meaning [(A x B) x B] x B) {text} biological status biol_stat The level of genome modification, e.g., wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant {text} chemical administration chem_administration list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603 {term}; {timestamp} collection method collection_method Process used to collect the sample, e.g., bronchoalveolar lavage (BAL) {text} depth depth Depth 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 can be reported as an interval for subsurface samples. {float} m derived from derived_from Indicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s) (SAMNxxxxxxxx). elevation elev The elevation of the sampling site as measured by the vertical distance from mean sea level. {float} {unit} experimental factor experimental_factor Variable aspect of experimental design {term|text} genetic modification genetic_mod Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection {text}|{PMID}|{DOI}|{URL} gravidity gravidity whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used {boolean};{timestamp} host age host_age Age of host at the time of sampling None host blood pressure diastolic host_blood_press_diast resting diastolic blood pressureof the host, measured as mm mercury {float} {unit} host blood pressure systolic host_blood_press_syst resting systolic blood pressure of the host, measured as mm mercury {float} {unit} host body habitat host_body_habitat original body habitat where the sample was obtained from {term} host body product host_body_product substance produced by the host, e.g. stool, mucus, where the sample was obtained from {text} host body temperature host_body_temp core body temperature of the host when sample was collected {float} {unit} host color host_color the color of host {text} host common name host_common_name The natural language (non-taxonomic) name of the host organism, e.g., mouse {text} host diet host_diet type of diet depending on the sample for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types {text} host disease host_disease Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh None host dry mass host_dry_mass measurement of dry mass {float} {unit} host family relationship host_family_relationship host genotype host_genotype host growth conditions host_growth_cond literature reference giving growth conditions of the host {PMID|DOI|URL} host height host_height the height of subject {float} {unit} host last meal host_last_meal content of last meal and time since feeding; can include multiple values {text};{period} host length host_length the length of subject {float} {unit} host life stage host_life_stage description of host life stage {text} host phenotype host_phenotype host sex host_sex Gender or physical sex of the host male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected | not provided | restricted access male female pooled male and female neuter hermaphrodite intersex not determined missing not applicable not collected not provided restricted access host shape host_shape morphological shape of host {text} host subject id host_subject_id a unique identifier by which each subject can be referred to, de-identified, e.g. #131 {text} host subspecific genetic lineage host_subspecf_genlin Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123 {rank name}:{text} host substrate host_substrate the growth substrate of the host {text} observed host symbionts host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host {text} host taxonomy ID host_taxid NCBI taxonomy ID of the host, e.g. 9606 {integer} host tissue sampled host_tissue_sampled name of body site where the sample was obtained from, such as a specific organ or tissue, e.g., tongue, lung. For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON None host total mass host_tot_mass total mass of the host at collection, the unit depends on host {float} {unit} metagenome source metagenome_source describes the original source of a metagenome assembled genome (MAG). Examples: soil metagenome, gut metagenome miscellaneous parameter misc_param any other measurement performed or parameter collected, that is not listed here {text};{float} {unit} negative control type neg_cont_type The substance or equipment used as a negative control in an investigation, e.g., distilled water, phosphate buffer, empty collection device, empty collection tube, DNA-free PCR mix, sterile swab, sterile syringe {text} Omics Observatory ID omics_observ_id A unique identifier of the omics-enabled observatory (or comparable time series) your data derives from. This identifier should be provided by the OMICON ontology; if you require a new identifier for your time series, contact the ontology's developers. Information is available here: https://github.com/GLOMICON/omicon. This field is only applicable to records which derive from an omics time-series or observatory. {term} organism count organism_count total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts {text};{float} {unit} oxygenation status of sample oxy_stat_samp oxygenation status of sample aerobic | anaerobic aerobic anaerobic perturbation perturbation type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types {text};{interval} positive control type pos_cont_type The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive {term} or {text} reference for biomaterial ref_biomaterial Primary publication or genome report {PMID|DOI|URL} relationship to oxygen rel_to_oxygen Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access aerobe | anaerobe | facultative | microaerophilic | microanaerobe | obligate aerobe | obligate anaerobe | missing | not applicable | not collected | not provided | restricted access aerobe anaerobe facultative microaerophilic microanaerobe obligate aerobe obligate anaerobe missing not applicable not collected not provided restricted access sample capture status samp_capt_status Reason for the sample, e.g., active surveillance in response to an outbreak, active surveillance not initiated by an outbreak, farm sample, market sample {text} sample collection device or method samp_collect_device Method or device employed for collecting sample {text} sample disease stage samp_dis_stage Stage of the disease at the time of sample collection, e.g., dissemination, growth and reproduction, infection, inoculation, penetration {text} sample material processing samp_mat_process Processing applied to the sample during or after isolation {text|term} sample salinity samp_salinity the amount of salt dissolved within the collected sample sample size samp_size Amount or size of sample (volume, mass or area) that was collected {float} {unit} sample storage duration samp_store_dur sample storage location samp_store_loc sample storage temperature samp_store_temp sample volume or weight for DNA extraction samp_vol_we_dna_ext volume (mL) or weight (g) of sample processed for DNA extraction {float} {unit} size fraction selected size_frac Filtering pore size used in sample preparation, e.g., 0-0.22 micrometer {term} source material identifiers source_material_id unique identifier assigned to 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. {text} temperature temp temperature of the sample at time of sampling {float} {unit}