host-associated_sample_data Sheet
Contextual data about the samples collected, such as when it was collected, where it was collected from, what kind of sample it is, and what were the properties of the host and host environment from which the sample was taken. Each row is a distinct sample. Most of this information is recorded during sample collection. Many terms have controlled vocabulary, such as organism, env_broad_scale, waterBody. This file contains information that is submitted to NCBI when generating a BioSample. Other important fields for metadata processing include amplicon_sequenced, which helps to link together different types of metdata. This sheet contains terms from the MIMARKS survey host-associated 6.0 package. For other types of samples (eg, sediment), use the appropriate template file.
| Term | Definition | Required by |
|---|---|---|
| depth | Depth is defined as the vertical distance below surface. Depth can be reported as an interval for subsurface samples. Provide depth in meters, eg: "5 " {float} {unit} | NCBI+OBIS |
| size_frac | Filtering pore size used in sample preparation | Optional |
| altitude | The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air. | Optional |
| 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 | Optional |
| elev | The elevation of the sampling site as measured by the vertical distance from mean sea level. | Optional |
| isolation_source | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. | Optional |
| misc_param | any other measurement performed or parameter collected, that is not listed here | Optional |
| 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 | Optional |
| 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. | Optional |
| 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 | Optional |
| oxy_stat_samp | oxygenation status of sample | Optional |
| perturbation | type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types | Optional |
| 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 | Optional |
| 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 | Optional |
| samp_store_dur | Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format | Optional |
| samp_store_loc | Location at which sample was stored, usually name of a specific freezer/room | Optional |
| samp_store_temp | Temperature at which sample was stored, e.g. -80 degree Celsius | Optional |
| temp | temperature of the sample at time of sampling | Optional |
| host | The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens". | NCBI |
| host_taxid | NCBI taxonomy ID of the host, e.g. 9606 | Recommended |
| host_subject_id | a unique identifier by which each subject can be referred to, de-identified, e.g. #131 | Recommended |
| host_sex | Gender of physical sex of the host | Optional |
| host_body_habitat | original body habitat where the sample was obtained from | Optional |
| 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) | Optional |
| biol_stat | The level of genome modification, e.g., wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant | Optional |
| 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 | Optional |
| gravidity | whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used | Optional |
| host_age | Age of host at the time of sampling | Optional |
| host_blood_press_diast | resting diastolic blood pressure of the host, measured as mm mercury | Optional |
| host_blood_press_syst | resting systolic blood pressure of the host, measured as mm mercury | Optional |
| host_body_product | substance produced by the host, e.g. stool, mucus, where the sample was obtained from | Optional |
| host_body_temp | core body temperature of the host when sample was collected | Optional |
| host_color | the color of host | Optional |
| host_common_name | The natural language (non-taxonomic) name of the host organism, e.g., mouse | Optional |
| host_diet | type of diet depending on the sample for animals omnivore, herbivore etc., for humans high-fat, mediterranean etc.; can include multiple diet types | Optional |
| 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 | Optional |
| host_fam_rel | Relationships to other hosts in the same study; can include multiple relationships | Optional |
| host_dry_mass | measurement of dry mass | Optional |
| host_genotype | Observed genotype | Optional |
| host_growth_cond | literature reference giving growth conditions of the host | Optional |
| host_height | the height of subject | Optional |
| host_last_meal | content of last meal and time since feeding; can include multiple values | Optional |
| host_length | the length of subject | Optional |
| host_life_stage | description of host life stage | Optional |
| host_phenotype | Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP) | Optional |
| host_shape | morphological shape of host | Optional |
| 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 | Optional |
| host_substrate | the growth substrate of the host | Optional |
| host_symbiont | The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host | Optional |
| 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 | Optional |
| host_tot_mass | total mass of the host at collection, the unit depends on host | Optional |
| 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 | Optional |
| samp_dis_stage | Stage of the disease at the time of sample collection, e.g., dissemination, growth and reproduction, infection, inoculation, penetration | Optional |
| samp_size | Amount or size of sample (volume, mass or area) that was collected | Optional |